273 lines
17 KiB
Text
273 lines
17 KiB
Text
<!DOCTYPE html>
|
|
<html lang="en">
|
|
<head>
|
|
<meta charset="UTF-8">
|
|
<title>/c/sequin/README</title>
|
|
<base href="//www.ncbi.nlm.nih.gov/IEB/ToolBox/C_DOC/lxr/">
|
|
<meta name="description" content="NCBI C Toolkit Cross Reference">
|
|
<meta http-equiv="cache-control" content="max-age=43200">
|
|
<link rel="stylesheet" href="//www.ncbi.nlm.nih.gov/corehtml/ncbi.css">
|
|
<link rel="stylesheet" type="text/css" href="lxr.css">
|
|
</head>
|
|
<body>
|
|
<h2 class="warning" style="padding:10pt">WARNING: C Toolkit is deprecated, please use C++ Toolkit instead</h2>
|
|
<header>
|
|
<div class="nav-menu">
|
|
<a href="/">NCBI Home</a><br>
|
|
<a href="/IEB/">IEB Home</a><br>
|
|
<a href="//www.ncbi.nlm.nih.gov/IEB/ToolBox/SDKDOCS/INDEX.HTML">C Toolkit docs</a><br>
|
|
<a href="/IEB/ToolBox/CPP_DOC/lxr/source">C++ Toolkit source browser</a><br>
|
|
</div>
|
|
<div class="nav-title">
|
|
<h1 class="main">NCBI C Toolkit Cross Reference</h1>
|
|
<h3 class="banner"><span class="banner"><a class="banner" href="/IEB/ToolBox/C_DOC/lxr/source/">c</a>/​<a class="banner" href="/IEB/ToolBox/C_DOC/lxr/source/sequin/">sequin</a>/​<a class="banner" href="/IEB/ToolBox/C_DOC/lxr/source/sequin/README">README</a></span></h3>
|
|
</div>
|
|
<div class="nav-mode">
|
|
<div><span class='modes-sel'>Source navigation</span><br><a class='modes' href="/IEB/ToolBox/C_DOC/lxr/diff/sequin/README">Diff markup</a><br><a class='modes' href="/IEB/ToolBox/C_DOC/lxr/ident">Identifier search</a><br><a class="modes" href="/IEB/ToolBox/C_DOC/lxr/search">General search</a><br></div>
|
|
</div>
|
|
</header>
|
|
<hr>
|
|
<main>
|
|
<p class="indexstate warning">
|
|
<i class=error>Warning, </i>/sequin/README<i class=error> is written in an unsupported language. File is not indexed.</i>
|
|
</p>
|
|
<div class="filecontent">
|
|
<pre class="filecontent-src">
|
|
SEQUIN APPLICATION
|
|
|
|
Sequin is a program designed to aid in the submission of sequences to the
|
|
GenBank, EMBL, and DDBJ sequence databases. It was written at the National
|
|
Center for Biotechnology Information, part of the National Library of
|
|
Medicine at the National Institutes of Health.
|
|
|
|
Sequin can assemble the essential elements of a GenBank record from simple
|
|
FASTA-format text files. For example, the program obtains the proper genetic
|
|
code from an organism name, and automatically determines coding region
|
|
intervals by back-translation from the protein sequence. An on-line help
|
|
window scrolls to the appropriate place as the user moves between and within
|
|
data entry forms, giving relevant details on what information is expected.
|
|
|
|
Sequin also contains a number of built-in validation functions for quality
|
|
assurance. Features such as splice sites and coding region translations are
|
|
checked for accuracy or internal consistency. Double-clicking on an error
|
|
message launches an appropriate editor by which the user can correct any
|
|
problems.
|
|
|
|
Sequin provides live, clickable views of the data in a variety of formats,
|
|
including a report form, GenBank flatfile, EMBL flatfile, and a graphical
|
|
view. Double clicking on an item in any of these formats launches an editor
|
|
for that item. The editor is capable of maintaining correct feature table
|
|
positions as the underlying sequence is edited. It can display features on
|
|
the sequence during editing, and allows feature intervals to be adjusted by
|
|
direct manipulation.
|
|
|
|
Sequin runs on Macintosh, PC/Windows, UNIX and VMS computers and is available
|
|
by anonymous ftp from ftp.ncbi.nih.gov.
|
|
|
|
|
|
ADDING ANALYSIS PROGRAMS TO SEQUIN
|
|
|
|
The seqncfig file can be configured to add items to Sequin's Analysis menu.
|
|
Each section gives instructions on how to constuct a URL query to send to a
|
|
cgi program on the Internet. The cgi program is then responsible for running
|
|
the desired analysis program and for any necessary format conversions. A
|
|
sample cgi program written in C, testcgi.c, is in the demo directory of the
|
|
NCBI software toolkit. A perl version will be available soon. (Some analysis
|
|
programs could be modified to act as cgi programs directly, and for those
|
|
cases a separate cgi mediator program would not be necessary.)
|
|
|
|
A portion of a sample seqncfig file is shown below. Note that the section
|
|
names for the services are specified in the [ORDER] section, and items must
|
|
be of the form ORDER_1, ORDER_2,...ORDER_n.
|
|
|
|
[ORDER]
|
|
ORDER_1=tRNAscan
|
|
ORDER_2=Seg
|
|
...
|
|
|
|
[tRNAscan]
|
|
HOST=www.myserver.myschool.edu
|
|
PORT=80
|
|
PATH=/MyServices/cgi-bin/testcgi.cgi
|
|
QUERY=request=trnascan
|
|
TITLE=tRNAscan-SE
|
|
SUBMENU=Search
|
|
FORMAT=FASTA
|
|
FLAGS=SEQ,NUC,TRG,NET
|
|
TIMEOUT=30
|
|
|
|
[Seg]
|
|
HOST=www.myserver.myschool.edu
|
|
PORT=80
|
|
PATH=/MyServices/cgi-bin/testcgi.cgi
|
|
QUERY_1=request=seg
|
|
TITLE_1=Seg default
|
|
QUERY_2=request=seg&window=10&lowcut=1.0&hicut=1.5
|
|
TITLE_2=Seg 10-1.0-1.5
|
|
QUERY_3=request=seg&window=12&lowcut=2.3&hicut=2.6
|
|
TITLE_3=Seg 12-2.3-2.6
|
|
SUBMENU=Seg
|
|
FORMAT=FASTA
|
|
FLAGS=SEQ,DOC,PRT,TRG,NET
|
|
TIMEOUT=30
|
|
...
|
|
|
|
[ENZYMES]
|
|
ENZ_1=BamHI
|
|
ENZ_2=EcoRI
|
|
ENZ_3=HindIII
|
|
|
|
The naming conventions for configuration files varies depending upon the
|
|
computer platform. For Mac it is seqncfig.cnf, for Windows seqncfig.ini, for
|
|
UNIX .seqncfigrc, and for VMS sequincfig.cfg. On the Mac, configuration files
|
|
go in the System Folder:Preferences folder, while for the PC they go in the
|
|
"windows" directory.
|
|
|
|
Individual configuration files may now be placed in a "services" directory
|
|
that is in the same directory as the Sequin program. They do not need to
|
|
conform to the naming convention described above.
|
|
|
|
|
|
SOLARIS EXECUTABLES
|
|
|
|
The Solaris executables distributed by NCBI no longer include a statically-
|
|
linked Motif library. This is due to the manner in which Sun distributes
|
|
Motif libraries. Users of Solaris version 2.4 and higher will find the
|
|
runtime shared Motif library on their system. Users of Solaris version 2.3
|
|
and earlier may need to either upgrade their systems or purchase the Motif
|
|
library separately.
|
|
|
|
It may be necessary to set your LD_LIBRARY_PATH environment variable to point
|
|
to the directory where this file, libXm.so.3 (the final digit may vary),
|
|
appears on your system. E.g.:
|
|
|
|
setenv LD_LIBRARY_PATH /usr/dt/lib
|
|
</pre>
|
|
<pre class="filecontent-num">
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/sequin/README#0001" name="0001">0001</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/sequin/README#0002" name="0002">0002</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/sequin/README#0003" name="0003">0003</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/sequin/README#0004" name="0004">0004</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/sequin/README#0005" name="0005">0005</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/sequin/README#0006" name="0006">0006</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/sequin/README#0007" name="0007">0007</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/sequin/README#0008" name="0008">0008</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/sequin/README#0009" name="0009">0009</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/sequin/README#0010" name="0010">0010</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/sequin/README#0011" name="0011">0011</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/sequin/README#0012" name="0012">0012</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/sequin/README#0013" name="0013">0013</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/sequin/README#0014" name="0014">0014</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/sequin/README#0015" name="0015">0015</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/sequin/README#0016" name="0016">0016</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/sequin/README#0017" name="0017">0017</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/sequin/README#0018" name="0018">0018</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/sequin/README#0019" name="0019">0019</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/sequin/README#0020" name="0020">0020</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/sequin/README#0021" name="0021">0021</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/sequin/README#0022" name="0022">0022</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/sequin/README#0023" name="0023">0023</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/sequin/README#0024" name="0024">0024</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/sequin/README#0025" name="0025">0025</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/sequin/README#0026" name="0026">0026</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/sequin/README#0027" name="0027">0027</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/sequin/README#0028" name="0028">0028</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/sequin/README#0029" name="0029">0029</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/sequin/README#0030" name="0030">0030</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/sequin/README#0031" name="0031">0031</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/sequin/README#0032" name="0032">0032</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/sequin/README#0033" name="0033">0033</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/sequin/README#0034" name="0034">0034</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/sequin/README#0035" name="0035">0035</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/sequin/README#0036" name="0036">0036</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/sequin/README#0037" name="0037">0037</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/sequin/README#0038" name="0038">0038</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/sequin/README#0039" name="0039">0039</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/sequin/README#0040" name="0040">0040</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/sequin/README#0041" name="0041">0041</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/sequin/README#0042" name="0042">0042</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/sequin/README#0043" name="0043">0043</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/sequin/README#0044" name="0044">0044</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/sequin/README#0045" name="0045">0045</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/sequin/README#0046" name="0046">0046</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/sequin/README#0047" name="0047">0047</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/sequin/README#0048" name="0048">0048</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/sequin/README#0049" name="0049">0049</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/sequin/README#0050" name="0050">0050</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/sequin/README#0051" name="0051">0051</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/sequin/README#0052" name="0052">0052</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/sequin/README#0053" name="0053">0053</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/sequin/README#0054" name="0054">0054</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/sequin/README#0055" name="0055">0055</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/sequin/README#0056" name="0056">0056</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/sequin/README#0057" name="0057">0057</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/sequin/README#0058" name="0058">0058</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/sequin/README#0059" name="0059">0059</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/sequin/README#0060" name="0060">0060</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/sequin/README#0061" name="0061">0061</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/sequin/README#0062" name="0062">0062</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/sequin/README#0063" name="0063">0063</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/sequin/README#0064" name="0064">0064</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/sequin/README#0065" name="0065">0065</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/sequin/README#0066" name="0066">0066</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/sequin/README#0067" name="0067">0067</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/sequin/README#0068" name="0068">0068</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/sequin/README#0069" name="0069">0069</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/sequin/README#0070" name="0070">0070</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/sequin/README#0071" name="0071">0071</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/sequin/README#0072" name="0072">0072</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/sequin/README#0073" name="0073">0073</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/sequin/README#0074" name="0074">0074</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/sequin/README#0075" name="0075">0075</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/sequin/README#0076" name="0076">0076</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/sequin/README#0077" name="0077">0077</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/sequin/README#0078" name="0078">0078</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/sequin/README#0079" name="0079">0079</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/sequin/README#0080" name="0080">0080</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/sequin/README#0081" name="0081">0081</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/sequin/README#0082" name="0082">0082</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/sequin/README#0083" name="0083">0083</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/sequin/README#0084" name="0084">0084</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/sequin/README#0085" name="0085">0085</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/sequin/README#0086" name="0086">0086</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/sequin/README#0087" name="0087">0087</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/sequin/README#0088" name="0088">0088</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/sequin/README#0089" name="0089">0089</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/sequin/README#0090" name="0090">0090</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/sequin/README#0091" name="0091">0091</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/sequin/README#0092" name="0092">0092</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/sequin/README#0093" name="0093">0093</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/sequin/README#0094" name="0094">0094</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/sequin/README#0095" name="0095">0095</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/sequin/README#0096" name="0096">0096</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/sequin/README#0097" name="0097">0097</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/sequin/README#0098" name="0098">0098</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/sequin/README#0099" name="0099">0099</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/sequin/README#0100" name="0100">0100</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/sequin/README#0101" name="0101">0101</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/sequin/README#0102" name="0102">0102</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/sequin/README#0103" name="0103">0103</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/sequin/README#0104" name="0104">0104</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/sequin/README#0105" name="0105">0105</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/sequin/README#0106" name="0106">0106</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/sequin/README#0107" name="0107">0107</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/sequin/README#0108" name="0108">0108</a>
|
|
<a class="fline" href="/IEB/ToolBox/C_DOC/lxr/source/sequin/README#0109" name="0109">0109</a>
|
|
</pre>
|
|
</div>
|
|
</main>
|
|
<footer>
|
|
<hr>
|
|
<div align="center">
|
|
[ <span class='modes-sel'>Source navigation</span> ] [ <a class='modes' href="/IEB/ToolBox/C_DOC/lxr/diff/sequin/README">Diff markup</a> ] [ <a class='modes' href="/IEB/ToolBox/C_DOC/lxr/ident">Identifier search</a> ] [ <a class="modes" href="/IEB/ToolBox/C_DOC/lxr/search">General search</a> ]
|
|
</div>
|
|
<hr>
|
|
<div class="version">
|
|
<span style="float:left">Generated by the LXR 2.3.5. – <span class=indexstate>Indexed on 2025-03-15 03:00:24 UTC</span>
|
|
</span>
|
|
<a style="float:right" href="https://www.hhs.gov/vulnerability-disclosure-policy/index.html">HHS Vulnerability Disclosure</a>
|
|
</div>
|
|
</footer>
|
|
<br>
|
|
</body>
|
|
</html>
|