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665 lines
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<!doctype html public "-//IETF//DTD HTML//EN">
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<TITLE>August 1994</TITLE>
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<body bgcolor="#f0f0f0">
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<META NAME="GENERATOR" CONTENT="Internet Assistant for Word 1.0Z">
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<META NAME="AUTHOR" CONTENT="The KEVRIC Company">
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</HEAD>
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<BODY>
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<P>
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<IMG SRC="/Gifs/newslogo.gif">
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<P>
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March 1996<HR>
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<P>
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<A NAME="toc"></A><A HREF="#OMIM">OMIM Database Available</A>
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<P>
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<A HREF="#Graphical">Entrez: Graphical Views of the Genomes Division </A>
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<P>
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<A HREF="#Sequin">Sequin Pre-Release</A>
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<P>
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<A HREF="#Secure">Entrez in Secure Environments</A>
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<P>
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<A HREF="#Blast">BLAST Service Update</A>
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<P>
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<A HREF="#CDROM">Entrez CD-ROM Discontinued</A>
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<P>
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<A HREF="#FAQ">Frequently Asked Questions</A>
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<P>
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<A HREF="#FTP">NCBI Data by FTP</A>
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<P>
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<A HREF="#Pubs">Recent Publications</A><HR>
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<H3><A NAME="OMIM">OMIM Database Now Available From NCBI </A>
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</H3>
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<P>
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Users of NCBI's World Wide Web (WWW) service may have noticed
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a recent addition to the NCBI Home Page, entitled "OMIM."
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The Online Mendelian Inheritance in Man database, or OMIM<SUP><SMALL>TM</SMALL></SUP>,
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is a continuously updated catalog of human genes and genetic disorders,
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and is considered a phenotypic companion to the human genome project.
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In December 1995, responsibility for providing public access to
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OMIM was transferred from the Genome Data Bank (GDB) at The Johns
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Hopkins University (JHU) to NCBI. It will continue to be authored
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and edited in the Center for Medical Genetics at JHU, under the
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direction of Dr. Victor McKusick, with computer support from NCBI.
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<P>
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<B>Web Link</B>
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<P>
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NCBI's Web service introduces new features that link OMIM entries
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to the Entrez integrated retrieval system, thereby providing easy
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access to related DNA and protein sequences as well as selected
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MEDLINE abstracts. In addition, NCBI's powerful "neighboring"
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feature for locating similar records has been applied to OMIM,
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allowing users to expand their searches at the touch of a button.
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OMIM's gene map, including clinical phenotypes, is also easily
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accessible and can be viewed in chart form, with direct links
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back to the full OMIM records.
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<P>
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<B>Searching OMIM</B>
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<P>
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The WWW address for the OMIM Home Page is "http://www.ncbi.nlm.nih.gov/omim".
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It can also be accessed from NCBI's Home Page. To initiate a keyword
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search or to view the OMIM gene map, go to the OMIM Home Page,
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and select the option "Search the OMIM Database."
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<P>
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For a keyword search, enter your search term in the text box,
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select data fields to be searched, then click on the "Submit
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Search" button. A list of all OMIM entries matching your
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search question will be displayed. Click on the OMIM identification
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number to see the full entry, which begins with a table of contents
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and list of available database links. For example, the entry for
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Huntington disease has a link to the OMIM gene map, plus 126 MEDLINE
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records, 2 protein sequence records, 4 DNA sequence records, 1
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GDB record, and 1 NCBI UniGene location. The full OMIM records
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contain sections on clinical features, case studies, inheritance,
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animal models, and more. Within the text are links to extensive
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references, most of which are further linked to MEDLINE abstracts.
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<P>
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To search the gene map, scroll down the query page to the section
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"View the OMIM Gene Map," enter a gene symbol or chromosomal
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location in the text box, then click the "Submit Search"
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button. A chart containing chromosomal location, descriptive title,
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associated disorders, and corresponding OMIM record numbers will
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be presented. To view the related OMIM text document, just click
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on the highlighted OMIM record numbers.
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<P>
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<B>Other Access Options</B>
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<P>
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OMIM is also accessible by e-mail through the NCBI Retrieve server
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(retrieve@ncbi.nlm.nih.gov). For information about using the Retrieve
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server, send the word HELP in the body of a message to the server
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address. The documentation will be sent to you automatically.
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If you have been a past user of OMIM through the IRX search system
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at GDB, you can obtain a new account and password to be used at
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NCBI. This approach is only recommended, however, for users who
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are unable to access the WWW version but do have telnet capability.
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If you are interested in downloading a full copy of the OMIM database
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for local use, it is available on NCBI's Anonymous FTP site (ncbi.nlm.nih.gov)
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in the "repository/OMIM" directory.
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<P>
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For additional information, please phone (301) 496-2475 or send
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e-mail to info@ncbi.nlm.nih.gov.
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<P>
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<A HREF="#toc">Return to Table of Contents</A><HR>
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<H3><A NAME="Graphical">Exploring Network Entrez: Graphical Views
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of the Genomes Division</A></H3>
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<P>
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In a major new release, several features have been added to Network
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Entrez, including a graphical sequence viewer that presents schematics
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of entire chromosomes, genomes, and associated map information
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available through the new Genomes Division of GenBank (see September
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1995 <I>NCBI News</I>). The Genomes Division currently contains
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more than 100 entries, including information on completely sequenced
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genomes and chromosomes such as <I>Haemophilus influenzae</I>
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and yeast, as well as contiged sequence islands from higher eukaryotes.
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Network Entrez presents chromosome level views of this data, then
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allows a chromosome subregion to be selected and enlarged to show
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a detailed graphical view of biological features annotated on
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that region.
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<P>
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The following step-by-step tutorial explores the use of Entrez's
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graphic display functions for Genomes Division searches. In this
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example, we will search for the location of the gene BRCA1 in
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the human genome. Starting with a chromosome level map view, we
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will use the "zoom" function to obtain an enlarged view
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of the specific chromosomal region containing BRCA1, then link
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to the corresponding GenBank record.
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<P>
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1. To access the Genomes Division, begin at the initial <B>Query</B>
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window of Network Entrez, and select <B>Genome</B> in the Database
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menu.
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<P>
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2. To search for the BRCA1 gene, select <B>Gene Symbol</B> in
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the Field menu, and <B>Selection</B> in the Mode menu. Then enter
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"BRCA1" (without quotes) in the <B>Term Entry Box</B>
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and press return. It should now appear alphabetically in the <B>Term
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Selection Box</B>. Double click on BRCA1 to include it in the
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<B>Query Refinement Box</B>.
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<P>
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3. Click on the <B>Retrieve</B> button to obtain the record for
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the chromosome containing the BRCA1, in this case <I>Homo sapiens</I>
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Chromosome 17.
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<P>
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4. Double click on the icon for Chromosome 17 to see the "map
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view" of this chromosome, shown below as Figure 1. (Tip:
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Enlarge the window for easier viewing.) The <B>Map</B> view is
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the default display mode in the Genomes Division. <B>Graphic</B>
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and <B>Alignment</B> views, shown as tabs at the top of the screen,
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are used to provide more detailed presentations of selected map
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regions.
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<P>
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As is the case with most higher eukaryotes, only small parts of
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human Chromosome 17 have been sequenced. For partially sequenced
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chromosomes, NCBI has collected several genetic and physical maps,
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placed them onto a common coordinate system, and aligned any shared
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markers (shown in Entrez by green connecting lines). In this example,
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the <B>Map</B> view shows the alignment of the MIT physical map,
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the NCBI transcript map, the CHLC linkage map, the Genethon linkage
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map, and the GDB cytogenetic map. Note that Stanford radiation
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hybrid maps will also be added as they become available; currently
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the Chromosome 4 map is in Entrez.
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<P>
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5. To find BRCA1 on the map, click on the <B>Find by Gene or Product
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Name</B> button, which will bring up a window with an alphabetical
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list of available markers located on Chromosome 17. This is a
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composite list of all markers that are included on at least one
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of the chromosome 17 maps used in Entrez. Enter BRCA1 in the text
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box (see Figure 1 inset) and click on the <B>Accept</B> button.
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<P>
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6. The <B>Map</B> view will be redrawn, and BRCA1 will now appear
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in red letters above the maps on which the marker is present.
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BRCA1 appears above the NCBI transcript map and the GDB cytogenetic
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map (see Figure 1 below).
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<P>
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<IMG SRC="17.gif" ALIGN="BOTTOM">
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<P>
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<I><A NAME="Fig1">Figure 1. </A>Map view</I>
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<P>
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7. To obtain a detailed view of the subregion containing BRCA1,
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we will use the graphic viewer "zoom" function. First,
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select one of the BRCA1 regions using a mouse technique called
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"rubber banding." That is, drag your cursor over the
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desired area while depressing the mouse button (see arrow on Figure 1).
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Then zoom in on the selected area by clicking on the <B>Graphic</B>
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tab. The <B>Graphic</B> view (see Figure 2 below) shows detailed features
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of the selected region and the positions of GenBank sequences that
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align to it.
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<P>
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<IMG SRC="17-2.gif" ALIGN="BOTTOM">
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<P>
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<I><A NAME="Fig2">Figure 2. Graphic view</A></I>
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<P>
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8. Scroll down to the GDB cytogenetic map (just past the Genethon
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map) and you will see BRCA1 in pink lettering with yellow highlighting,
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as well as a list of the other markers that have been mapped to
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the same region. All the markers appearing in pink lettering have
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links to corresponding DNA sequence, protein sequence, or MEDLINE
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records (but MEDLINE links are not yet implemented). Double click
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on BRCA1 and the corresponding GenBank record will appear.
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<P>
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This example illustrates just a few of the many features available
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with Entrez's new graphical viewing functions, and focuses only
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on locating a gene within an incompletely sequenced chromosome.
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Note that, for completely sequenced genomes and chromosomes, <B>Map</B>
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and <B>Graphic</B> view presentation details will differ from
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this example. However, the ability to go to successively more
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detailed displays, using the <B>Map</B>, <B>Graphic</B>, and <B>Alignment</B>
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views, is a basic feature of the Genomes Division in Entrez. The
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<B>Alignment</B> view, not discussed in the BRCA1 example, shows
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the relationship of sequences aligned at base pair resolution
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in cases where multiple database sequences map to the same region.
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<P>
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Network Entrez users are encouraged to explore these new features
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and contact NCBI with any questions or suggestions. The new release
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of Network Entrez is located in the "entrez/network"
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directory on NCBI's Anonymous FTP site (ncbi.nlm.nih.gov). The
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graphical viewing functions have not yet been implemented in the
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World Wide Web version of Entrez.
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<P>
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<A HREF="#toc">Return to Table of Contents</A><HR>
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<H3><A NAME="Sequin">Sequin Pre-Release Available for Testing</A>
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</H3>
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<P>
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NCBI is now making available a beta-test version of Sequin, a
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new stand-alone software tool for submitting and updating GenBank
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entries. Intended as an alternative to Authorin, Sequin is designed
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to simplify the sequence submission process, provide graphical
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viewing and editing options, and provide increased data handling
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capabilities. New data handling features include the ability to
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submit segmented entries, annotate protein features, perform data
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integrity checks, and accommodate bulk submissions. The graphical
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viewing function offers an inviting and easy-to-use interface.
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<P>
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Sequin also produces submission files suitable for use by the
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international collaborating databases (EMBL and DDBJ), and is
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currently being reviewed and tested by them to ensure full compatibility.
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<P>
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NCBI invites submitters to participate in testing Sequin and encourages
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feedback and comments. Although a beta-test version, the Sequin
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pre-release is a full-featured submission tool that you can use
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now for actual GenBank submissions. The beta-test version is available
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for Macintosh, PC/Windows, UNIX, and VMS computers and is available
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by Anonymous FTP from ncbi.nlm.nih.gov in the "sequin"
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directory.
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<P>
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<A HREF="#toc">Return to Table of Contents</A><HR>
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<H3><A NAME="Secure">Using Entrez in Secure Environments</A></H3>
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<P>
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Many users have expressed interest in using Network Entrez through
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institutional security systems, such as a firewall. A firewall
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restricts an internal network's contact with outside networks
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to varying degrees. This article describes some of the technical
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issues and solutions for implementing Network Entrez in a secure
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environment. You may need the cooperation and assistance of your
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local systems administrator to implement these solutions.
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<P>
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<B>Operating Through a Firewall</B>
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<P>
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NCBI has recently enhanced Network Entrez (versions 4.013 and
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higher) to allow users to configure it for use through a firewall.
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In the default mode of a client-server application such as Network
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Entrez, the server connects to the client. However, it is possible
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to reverse the direction of the client-server connection, causing
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the client to connect to the server. This arrangement is usually
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much more favorable to firewalls.
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<P>
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When configuring Network Entrez, you can override the default
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direction and reverse the connection in one of two ways: (1) select
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the "Outgoing connections only" checkbox on the second
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screen of the "netentcf" configuration program; or (2)
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manually set DIRECT_SVC_CON=TRUE in the [NET_SERV] section of
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the NCBI configuration file on your system. In addition, in the
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"netentcf" configuration program, you will still need
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to establish the two TCP/IP connections to NCBI and the Network
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Entrez server. To confirm that the default direction has been
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reversed, open Network Entrez and select the "More"
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button under "About Entrez." You should see the phrase
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"Using outgoing connection when communicating with server."
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<P>
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If neither of the two approaches successfully enables Network
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Entrez to operate through your institutional firewall, contact
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NCBI for information on additional technical solutions currently
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under development. You may also wish to compile Network Entrez
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for yourself from source code if you have an institutional firewall
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that requires special treatment. Source code is available in the
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NCBI toolbox (ftp ncbi.nlm.nih.gov/toolbox/ncbi_tools).
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<P>
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<B>Using SOCKS Protocol</B>
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<P>
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NCBI intends to continue supporting SOCKS capability, but only
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for the Unix platforms. SOCKS is a well-defined protocol that
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permits client-server applications to transparently and securely
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traverse firewalls by providing an additional layer between the
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application and transport layers. There are no plans to add any
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SOCKS capability for non-UNIX platforms. But note that on Windows
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platforms it is possible, in principle, for a SOCKS-friendly WinSock
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implementation to provide SOCKS-based Network Entrez access when
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used in combination with the DIRECT_SVC_CON mode described above.
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<P>
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<B>Using Data Encryption</B>
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<P>
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Another security option is to build an encrypted version of Network
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Entrez. You will need to build the client from scratch by using
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the source code from the NCBI toolbox and following directions
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provided in the file 'network/encrypt/README'. Note that the RSA
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and DES encryption technology may not be exported outside the
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United States and Canada, and therefore we are unable to offer
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encryption-enabled binaries for FTP.
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<P>
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<A HREF="#toc">Return to Table of Contents</A><HR>
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<H3><A NAME="Blast">BLAST Service Update</A></H3>
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<P>
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Several changes in the BLAST service went into effect on March
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11. These include reorganization of databases, new client software,
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changes in sequence identifier format, and new databases available
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by FTP.
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<P>
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<B>Database Reorganization</B>
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<P>
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The BLAST databases have been reorganized for more efficient searching
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and better synchronization with Entrez. In order to give users
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more control over their BLAST searches, the EST and STS sequences
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have been eliminated from the "nr" (nonredundant) database,
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and now exist as separate data sets that can be selected for searching.
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In addition, a new database called "month" contains
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new or revised sequences released in the last 30 days, providing
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a rolling 30-day window of the newest sequences.
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<P>
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<B>Sequence Identifiers</B>
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<P>
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The one-line description used in BLAST output for GenBank conceptual
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translations has changed with respect to the sequence identifier
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number. In order to identify each specific protein sequence, NCBI
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is now assigning a stable identifier called a "gi" number
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for all sequences, both protein and nucleotide. The "gi"
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is a unique integer that changes whenever the sequence changes,
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but not when the features or references of an entry are updated.
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<P>
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The new format for protein sequence one-line descriptions starts
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with the label "gi," followed by the gi number, the
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accession number in parens, and the text description, for example:
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"gi|451623 (U04987) env gene product [Simian immunodef...]."
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<P>
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<B>New Blast2 Client</B>
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<P>
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For users of Network BLAST, a new client called Blast2 has been
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introduced that provides a better interface for postprocessing
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of search results. Blast2 represents the foundation for NCBI's
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future development of the BLAST service. Although the older client,
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known as "Experimental Blast," will operate with the
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new database organization, users are encouraged to upgrade to
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Blast2, which is available on the FTP site (ncbi.nlm.nih.gov)
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in the "blast/network/blast2" directory.
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<P>
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<B>Performance Improvements</B>
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<P>
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Many users have noticed that, over the past several months, BLAST
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searches have taken much longer to complete. This is due to an
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increase in the number of searches and in the size of the database.
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We are taking several steps to improve performance in addition
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to the reorganization of the databases. First, we will be upgrading
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the processors in the BLAST servers within the next 6 weeks, which
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should double the speed of typical jobs. Second, the operating
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system and queuing software are being tuned for greater efficiency.
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And finally, algorithm improvements to BLAST are being tested
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and are expected to yield up to fivefold performance gains for
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protein searches. Gradual improvements in search times over the
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next several months are expected.
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<P>
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<B>Databases on FTP Site</B>
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<P>
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For those users who wish to implement the BLAST search engines
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in-house, all of the databases, including the nonredundant DNA
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and protein sequence databases, are available as FASTA files from
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the NCBI FTP site (ncbi.nlm.nih.gov) in the "blast/db"
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directory.
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<P>
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<A HREF="#toc">Return to Table of Contents</A><HR>
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<H3><A NAME="CDROM">Entrez CD-ROM To Be Discontinued </A></H3>
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<P>
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After careful consideration, NCBI has decided to discontinue the
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Entrez CD-ROM effective August 15, 1996, with Release 24. Due
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to the continuing rapid growth of GenBank and other sequence databases,
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the five-disc version of Entrez has become increasingly inconvenient
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to use. For some time now, the CD-ROM version has lagged behind
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the two Internet versions, Network Entrez and World Wide Web Entrez,
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in several aspects. Differences include update frequency; number
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of MEDLINE citations available; incorporation of new data sets
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such as genetic maps and 3D structures; and links to online journals.
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The Internet versions are updated daily, while the CD-ROM version
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is only updated every other month. The considerable advantages
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of the Internet versions of Entrez have resulted in a sustained
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increase in use, with simultaneous decline in CD-ROM subscriptions,
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from a peak of more than 2,200 subscribers to less than 1,400
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today.
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<P>
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Impact on domestic and non-U.S. CD-ROM users was assessed through
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a survey conducted by NCBI in December 1994. Results showed that
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more than 70 percent of U.S. users and more than 50 percent of
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non-U.S. subscribers were willing to switch to an Internet version.
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An additional 20 percent indicated they would switch to Internet
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alternatives as the number of discs per Entrez release approached
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five. Entrez now uses five discs and the August 1996 release is
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expected to require six or more.
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<P>
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Access to the Internet versions of Entrez is simple. Many users
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have free high-speed Internet access through their academic institutions
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or companies, and dial-up access is available almost anywhere
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in the United States for $15-$25 per month. If you have a World
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Wide Web browser such as Netscape or Mosaic, simply point your
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browser to "http://www.ncbi.nlm.nih.gov/." The Web version
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of Entrez has all the capabilities of the CD-ROM version, but
|
|
with the visual style of the World Wide Web. If you prefer the
|
|
"look and feel" of the CD-ROM version, you may download
|
|
Network Entrez from the NCBI's Anonymous FTP site (ncbi.nlm.nih.gov).
|
|
Network Entrez offers all the advantages of Web Entrez. Versions
|
|
are available for PC/Windows, Macintosh, and several Unix workstations
|
|
in the "entrez/network" directory.
|
|
<P>
|
|
The last release of Entrez on CD-ROM will be on August 15, 1996.
|
|
If you choose to renew your subscription between now and then,
|
|
the Government Printing Office (GPO) will charge you the full
|
|
six-issue cost. You must request a pro-rated refund from the GPO
|
|
for any amount that will be due to you after the final release.
|
|
<P>
|
|
<A HREF="#toc">Return to Table of Contents</A><HR>
|
|
|
|
<H3><A NAME="FAQ">Frequently Asked Questions</A></H3>
|
|
|
|
<P>
|
|
<I>I have noticed a new NID (nucleotide id) field in GenBank.
|
|
What does this number indicate?</I>
|
|
<P>
|
|
The NID field is used specifically for NCBI's nucleotide sequence
|
|
identifier, called an "NID gi." Previously, this number
|
|
was included in the COMMENT field, but beginning with Release
|
|
94.0, it will appear only in the new NID field.
|
|
<P>
|
|
An NID gi number is assigned to every nucleotide sequence in GenBank.
|
|
A new number is issued whenever a revision is made in the DNA
|
|
sequence data. In this way it differs from the accession number,
|
|
which is a stable identifier that does not change when modifications
|
|
are made to the record.
|
|
<P>
|
|
<I>I was making a submission using BankIt and my system crashed.
|
|
Can I get a copy of the data I have prepared so far?</I>
|
|
<P>
|
|
If you clicked the BankIt button at least once when you were entering
|
|
your data, the information was transmitted to our logs and a BankIt
|
|
processing number was assigned to your submission. In this case,
|
|
we can retrieve a copy of your file in HTML format and send it
|
|
to you by e-mail. You can then load it into your WWW browser and
|
|
continue your submission.
|
|
<P>
|
|
<I>I have a number of submissions to make and would like my accession
|
|
numbers in consecutive order. Is this possible?</I>
|
|
<P>
|
|
If you are using BankIt, the following prompt appears at the beginning
|
|
of the BankIt form: "This submission is number __ of a set
|
|
of __ submission(s)." Indicate the number of sequences you
|
|
intend to submit, and the GenBank staff will wait for the entire
|
|
batch before assigning a block of accession numbers.
|
|
<P>
|
|
If you are using Authorin to submit by e-mail, include a message
|
|
at the beginning of your submission stating how many .sbt files
|
|
you are sending, and indicate that you would like sequential accession
|
|
numbers. If you are submitting more than 20 sequences, please
|
|
divide up the submission into separate messages containing no
|
|
more than 20 files each. This will facilitate our processing,
|
|
and you will still receive sequential accession numbers.
|
|
<P>
|
|
<I>What is the difference between dbEST and the EST Division of
|
|
GenBank? Are the sequence records different?</I>
|
|
<P>
|
|
The sequences and accession numbers in dbEST are identical to
|
|
those in the EST Division of GenBank. The dbEST database, however,
|
|
contains additional annotation not found in GenBank, such as information
|
|
on the clone library, sequencing method, map location if known,
|
|
sources for obtaining the physical clone, and results of BLAST
|
|
sequence similarity searches.
|
|
<P>
|
|
<I>Using OMIM, if I know the chromosome location of a disorder,
|
|
is it possible to see diseases and disorders in this same region?</I>
|
|
|
|
<P>
|
|
Yes, this is possible by using the Gene Map section of OMIM. From
|
|
the OMIM Home Page, select "Search the OMIM Database,"
|
|
then scroll down to the section "View the OMIM Gene Map"
|
|
on the search page. Enter the chromosome location, and click on
|
|
"View." A table including map location, gene symbols,
|
|
OMIM number, and associated disorder information will be presented.
|
|
<P>
|
|
<I>Once I've located an OMIM record I am interested in, how do
|
|
I find out if there is a known map location?</I>
|
|
<P>
|
|
Each OMIM record starts with a Table of Contents, under which
|
|
is an array of buttons indicating cross-database links. The "Gene
|
|
Map" button indicates that mapping information is available,
|
|
and the location will also be displayed under the line of buttons.
|
|
To see the Gene Map, click on the button.
|
|
<P>
|
|
<A HREF="#toc">Return to Table of Contents</A><HR>
|
|
|
|
<H3><A NAME="FTP">NCBI Data by FTP</A></H3>
|
|
|
|
<P>
|
|
The NCBI FTP site contains a variety of directories with publicly
|
|
available databases and software. The available directories include
|
|
"repository", "genbank", "entrez",
|
|
"toolbox", and "pub".
|
|
<P>
|
|
The <B>repository</B> directory makes a number of molecular biology
|
|
databases available to the scientific community. This directory
|
|
includes databases such as PIR 47.00, Swiss-Prot, CarbBank, AceDB,
|
|
and FlyBase.
|
|
<P>
|
|
The <B>genbank</B> directory contains files with the latest full
|
|
release of Genbank, the daily cumulative updates, and the latest
|
|
release notes.
|
|
<P>
|
|
The <B>entrez</B> directory contains the Entrez executable programs
|
|
for accessing CD-ROM data on a variety of platforms. It also contains
|
|
client software for Network Entrez.
|
|
<P>
|
|
The <B>toolbox</B> directory contains a set of software and data
|
|
exchange specifications that are used by NCBI to produce portable
|
|
software, and includes ASN.1 tools and specifications for molecular
|
|
sequence data.
|
|
<P>
|
|
The <B>pub</B> directory offers public-domain software, such as
|
|
BLAST (sequence similarity search program), MACAW (multiple sequence
|
|
alignment program), and Authorin submission software for Mac and
|
|
PC systems. Client software for Network BLAST is also included
|
|
in this directory.
|
|
<P>
|
|
Data in these directories can be transferred through the Internet
|
|
by using the Anonymous FTP program. To connect, type: <B>ftp ncbi.nlm.nih.gov</B>
|
|
or <B>ftp 130.14.25.1</B>. Enter anonymous for the login name,
|
|
and enter your e-mail address as the password. Then change to
|
|
the appropriate directory. For example, change to the repository
|
|
directory (cd repository) to download specialized databases.
|
|
<P>
|
|
<A HREF="#toc">Return to Table of Contents</A><HR>
|
|
|
|
<H3><A NAME="Pubs">Selected Recent Publications by NCBI Staff</A>
|
|
</H3>
|
|
|
|
<P>
|
|
Ahmad, N, BM Baroudy, RC Baker, and <B>C Chappey</B>. Genetic
|
|
analysis of immunodeficiency virus type 1 envelope V3 region isolates
|
|
from mother and infant isolates after perinatal transmission.
|
|
<I>J Virol</I> 69(2):1001-12, 1995.
|
|
<P>
|
|
<B>Bassett DE</B>, <B>MS Boguski</B>, F Spencer, R Reeves, M Goebl,
|
|
and P Hieter. Comparative genomics, genome cross-referencing and
|
|
XREFdb. <I>Trends Genet</I> 11:372-3, 1995.
|
|
<P>
|
|
<B>Baxevanis, AD</B>, and <B>D Landsman</B>. Histone sequence
|
|
database: a compilation of highly-conserved nucleoprotein sequences<I>.
|
|
Nucleic Acids Res</I> 24(1):245-7, 1995.
|
|
<P>
|
|
Gunderson, J, G Hinkle, <B>D Leipe</B>, HG Morrison, SK Stickel,
|
|
DA Odelson, JA Breznak,TA Nerad, M Mueller, and ML Sogin. Phylogeny
|
|
of trichomonads inferred from small subunit rRNA sequences. <I>J
|
|
Eukaryot Microbiol</I> 42:411-5, 1995.
|
|
<P>
|
|
<B>Koonin, EV</B>, <B>RL Tatusov</B>, and <B>KE Rudd</B>. Sequence
|
|
similarity analysis of<I> Escherichia coli</I> proteins--functional
|
|
and evolutionary implications. <I>Proc Natl Acad Sci USA</I> 92:11921-5,
|
|
1995.
|
|
<P>
|
|
Kulaeva, OI, <B>JC Wootton</B>, AS Levine, and R Woodgate. Characterization
|
|
of the umu-complementing operon from R391. <I>J Bacteriol</I>
|
|
177:2737-43, 1995.
|
|
<P>
|
|
Liu, JS, <B>AF Neuwald</B>, and <B>CE Lawrence</B>. Bayesian models
|
|
for multiple local sequence alignment and Gibbs sampling strategies.
|
|
<I>J Am Stat Assoc</I> 90:1156-70, 1995.
|
|
<P>
|
|
<B>Madei, T</B>, <B>MS Boguski</B>, and <B>SH Bryant</B>. Threading
|
|
analysis suggests that the obese gene product may be a helical
|
|
cytokine. <I>FEBS Lett</I> 373:13-8, 1995.
|
|
<P>
|
|
<B>Mushegian, AR</B>, and RJ Shepherd. Genetic elements of plant
|
|
viruses as tools for genetic engineering. <I>Microbiol Rev</I>
|
|
59:548-78,1995.
|
|
<P>
|
|
<B>Neuwald, AF</B>, and P Green. Detecting patterns in protein
|
|
sequences. <I>J Mol Biol</I> 239:698-712, 1995.
|
|
<P>
|
|
Wu, SC, <B>JL Spouge</B>, SL Conley, WP Tsai, and PL Na. Human
|
|
plasma enhances the infectivity of primary human immunodeficiency
|
|
virus type 1 isolates in peripheral blood mononuclear cells and
|
|
monocyte-derived macrophages. <I>J Virol</I> 69:6054-62, 1995.
|
|
<P>
|
|
<A HREF="#toc">Return to Table of Contents</A><HR>
|
|
|
|
<H4><A NAME="Masthead">Masthead</A></H4>
|
|
|
|
<P>
|
|
<I>NCBI News</I> is distributed three times a year. We welcome
|
|
communication from users of NCBI databases and software and invite
|
|
suggestions for articles in future issues. Send correspondence
|
|
and suggestions to <I>NCBI News</I> at the address below.
|
|
<P>
|
|
<I>NCBI News<BR>
|
|
</I>National Library of Medicine<BR>
|
|
Bldg. 38A, Room 8N-803<BR>
|
|
8600 Rockville Pike<BR>
|
|
Bethesda, MD 20894<BR>
|
|
Phone: (301) 496-2475<BR>
|
|
Fax: (301) 480-9241<BR>
|
|
E-mail: info@ncbi.nlm.nih.gov
|
|
<P>
|
|
<I>Editors<BR>
|
|
</I>Dennis Benson<BR>
|
|
Barbara Rapp
|
|
<P>
|
|
<I>Design Consultant<BR>
|
|
</I>Troy M. Hill
|
|
<P>
|
|
<I>Photography<BR>
|
|
</I>Karlton Jackson
|
|
<P>
|
|
<I>Editing, Graphics, and Production<BR>
|
|
</I>Veronica Johnson<BR>
|
|
Deborah Loer-Martin<BR>
|
|
Wendy B. Osborne
|
|
<P>
|
|
In 1988, Congress established the National Center for Biotechnology
|
|
Information as part of the National Library of Medicine; its charge
|
|
is to create automated systems for storing molecular biology,
|
|
biochemistry, and genetics data, and to perform research in computational
|
|
molecular biology.
|
|
<P>
|
|
The contents of this newsletter may be reprinted without permission.
|
|
The mention of trade names, commercial products, or organizations
|
|
does not imply endorsement by NCBI, NIH, or the U.S. Government.
|
|
<P>
|
|
NIH Publication No. 96-3272<BR>
|
|
ISSN 1060-8788
|
|
<P>
|
|
<A HREF="#toc">Return to Table of Contents</A>
|
|
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