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203 lines
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11 KiB
HTML
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<title>NCBI News | Spring 2002</title>
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<span class="heads"></span> <span class="subheads"></span>
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<td height="176" colspan="2" valign="left" align="left"><img height="12" width="8" src="images/dotclear.gif" alt=" "><img height="171" width="173" src="images/logo.gif" alt="NCBI Logo"></td>
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<td height="176" valign="top" width="420"><img height="80" width="364" src="images/msthd1.gif" border="0" alt="NCBI News" usemap="#E">
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<td height="80"><img height="80" width="340" src="images/msthd1a.gif" border="0" alt="National Center for Biotechnology Information" usemap="#NCBI">
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<td height="80"><img height="80" width="80" alt="Spring 2002" src="images/edition.gif"></td>
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</tr>
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</table>
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</td>
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</tr>
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<tr valign="top">
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<td width="13" align="left" valign="top"><img height="10" width="13" src="images/dotclear.gif" alt=" "></td>
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<td width="173" align="left" valign="top">
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<p><br>
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<br>
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<img height="33" width="178" src="images/issue.gif" alt="In this issue..."><br>
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<br>
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<span class="navon">Model Maker</span><br>
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<br>
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<a href="virus.html" class="navoff">Virus Reference<br>
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Sequences</a><br>
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<br>
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<a href="virus.html" class="navoff">Release of the<br>
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1,000th Virus<br>
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Reference Genome</a><br>
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<br>
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<a href="mapviewer.html" class="navoff">New MapViewer<br>
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Displays</a><br>
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<br>
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<a href="mapviewer.html" class="navoff">Other Genomic<br>
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MapViews</a><br>
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<br>
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<a href="mouse.html" class="navoff">Mouse Genome<br>
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BLAST</a><br>
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<br>
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<a href="mouse.html" class="navoff">New Genomes<br>
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in GenBank</a><br>
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<br>
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<a href="organism.html" class="navoff">Organism-Specific<br>
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BLAST</a><br>
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<br>
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<a href="protest.html" class="navoff">ProtEST</a><br>
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<br>
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<a href="protest.html" class="navoff">Trace Archive<br>
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Expands</a><br>
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<br>
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<a href="blast.html" class="navoff">BLAST Lab</a><br>
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<br>
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<a href="findout.html" class="navoff">Find Out<br>
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“About NCBI”</a><br>
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<br>
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<a href="newftp.html" class="navoff">New FTP<br>
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Hierarchy</a><br>
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<br>
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<a href="barbara.html" class="navoff">Barbara Rapp<br>
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Leaves NCBI</a><br>
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<br>
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<a href="masthead.html" class="navoff">Masthead</a></p>
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</td>
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<td width="10" valign="left" bordercolor="003399"> </td>
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<td width="420" bordercolor="003399">
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<div valign="left">
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<p><img height="25" width="8" src="images/dotclear.gif" alt=" "><br>
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<span class="headlines"><b class="headlines">Make Your Own Gene Models
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with Model Maker</b></span></p>
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<br>
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<span class="bodycopy">The Model Maker is a tool that allows the construction
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of an mRNA sequence model using putative exons defined by <i>ab initio</i>
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prediction and by aligning GenBank® transcripts (including ESTs)
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and NCBI RefSeqs to the NCBI human genome assembly. The ability to generate
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alternative transcript models using novel combinations of exons not
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represented in any single mRNA sequence alignment is useful in the exploration
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of gene model variants.<br>
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</span> <span class="bodycopy"> <br>
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To generate a Model Maker display centered on a gene of interest, go
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to the Human Map Viewer page (Model Maker links will soon be available
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directly from LocusLink) and type the gene symbol or gene name into
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the query box. Select the Genes_seq map as the Master Map and click
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on the “mm” link to the right of the gene name. The Model
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Maker display for the HOXB1 gene is shown in Figure 1 below. The gene
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is found on the RefSeq contig NT_010783.9, with the chromosome coordinates
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shown. You may move upstream or downstream from the contig using a pair
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of horizontal arrows. If you click on the sequence viewer link “sv”
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after this repositioning, you will be able to see the upstream or downstream
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sequences of the contig. <br>
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<br>
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</span> <span class="bodycopy"> The Model Maker page is divided into
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several sections. The first section displays “evidence” for
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exons in the form of sequence records from the databases that have been
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aligned to human genome assembly contig NT_010783.9 to produce the NCBI
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gene model for HOXB1. These sequences include, from top to bottom, a
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GenBank mRNA sequence and the mRNA RefSeq derived from it, each contributing
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2 exons; a GenomeScan-generated model, contributing an additional small
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exon; and a genomic RefSeq derived from the alignment of the mRNA RefSeq
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with the contig, contributing 2 exons.<br>
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<br>
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The Model Maker gathers the unique putative exons from the various alignments
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used as evidence, assigns each a consecutive number, and presents them
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in a “graphic view”. In the Figure, three unique exons are
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shown in the “graphic view” which may be added or removed
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from the nascent model by clicking them on or off. By choosing the “hits”
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hyperlink next to an evidence sequence, the coordinates of BLAST®
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hits for the evidence sequence on the human genomic sequence are shown
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and intron lengths may be deduced. It is also possible to select whole
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“exon sets” from evidence mRNAs, using the “set”
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link, add EST alignments to the evidence list, extend the region shown
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downstream and upstream or switch to the opposite strand.<br>
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</span><br>
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<a href="#" onClick="MM_openBrWindow('model_lrg.html','Figure','scrollbars=yes,width=580,height=523')"><img src="images/model_sm.gif" width="420" height="373" border="1" alt=""><br></a>
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<table width="438" border="0" cellspacing="1" cellpadding="0">
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<tr>
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<td height="25" align="center" class="tables2">Click on figure to
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view enlarged version</td>
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</tr>
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</table>
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<a href="#" onClick="MM_openBrWindow('model_lrg.html','Figure','scrollbars=yes,width=580,height=523')"><br>
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</a><span class="captions">Figure 1: </span><span class="captions2">Model
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Maker display for HOX1B located on contig NT_010783.9. Access the Contig
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record by clicking the Accession Number hyperlink NT_010783.9. Move upstream
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or downstream by clicking on the arrows: <<< (upstream) or >>>
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(downstream). View the opposite strand by clicking on “change strand”
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hyperlink. Select “set” to select an evidence record as your
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model. Select “add ESTs” to add a graphical display of ESTs.
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To build a custom model, select the exon or EST of interest by clicking
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on the graphic view segment or select the exon from the table by using
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a check box. Monitor the growing model by viewing its translation in three
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different reading frames. The longest ORF in each frame is denoted by
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UPPERCASE letters. Save your results by clicking on the “Save”
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hyperlink.</span><br>
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<br>
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<span class="bodycopy"> The information in the “graphic view”
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is also presented as a “table view” that gives the start and
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stop positions of each putative exon, along with the first three and
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last three bases of each exon and two bases immediately upstream and
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downstream of the exon. Exons are selected for inclusion in the model
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using check boxes. Numbered links at the ends of each exon facilitate
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the selection of adjacent exons implied by existing transcripts. As
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each exon is selected, the 3- frame trans-lations of the model sequence
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are updated in the ORF Frames boxes. The longest ORF in each translation
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is shown in UPPER CASE letters. As compatible exons are added to the
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model, in phase, an ORF in at least one of the three reading-frames
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lengthens. When the stop codon is reached and the model is complete,
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it may be saved to a local file in FASTA format for use with other programs. </span><span class="authors">—EP,
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MB</span><span class="bodycopy"><br>
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</span><br>
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<br>
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<p align="right"><a href="virus.html"><img height="27" width="69" src="images/continue.gif" border="0" alt="Continue"></a><br>
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<div align="right"></div>
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<hr noshade size="1" align="right" width="420">
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<div align="right"><img height="32" width="177" border="0" alt="NCBI News | Spring 2002" usemap="#NCBI News foot" src="images/foot.gif">
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<br>
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<br>
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</div>
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<p class="body_text"></p>
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</div>
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</td>
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