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ORFfinder requires JavaScript to function.
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<a href="/guide/browsers/#enablejs" title="Learn how to enable JavaScript" target="_blank">more...</a>
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<h1 class="rusted">Open Reading Frame Finder</h1>
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<p class="textj">ORF finder searches for open reading frames (ORFs) in the DNA sequence you enter. The program returns the range of each ORF, along with its protein translation. Use ORF finder to search newly sequenced DNA for potential protein encoding segments, verify predicted protein using newly developed SMART BLAST or regular BLASTP.</p>
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<p class="textj">This web version of the ORF finder is limited to the subrange of the query sequence up to 50 kb long. Stand-alone version, which doesn't have query sequence length limitation, is available for <a href="https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/ORFfinder/linux-i64/" title="Download the executable from NCBI FTP site">Linux x64</a>.</p>
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<p class="textj"><b>Examples</b> (click to set values, then click Submit button) :</p>
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<ul id="examplelist">
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<li><a class="RegularLink example" idx="0">NC_011604 Salmonella enterica plasmid pWES-1; genetic code: 11; 'ATG' and alternative initiation codons; minimal ORF length: 300 nt</a></li>
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<li><a class="RegularLink example" idx="1">NM_000059; genetic code: 1; start codon: 'ATG only'; minimal ORF length: 150 nt</a></li>
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</ul>
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</div>
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</div>
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<form action="" method="post" enctype="multipart/form-data">
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<input type="hidden" name="csrfmiddlewaretoken" value="vElnQZFXjStzoKEM26pmOvFT9oHNDFOvFzyKtupNVMM4IqhsK1c2exUprmZrsOvz">
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<fieldset>
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<legend>Enter Query Sequence</legend>
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<div class="field">
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<label for="id_acc">Enter accession number, gi, or nucleotide sequence in FASTA format:</label>
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<a class="helplink jig-ncbitoggler ui-ncbitoggler" data-ncbitoggler-toggles="hq" title="How to enter the sequence data" href="#" id="Help_query">
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<span>[?]</span>
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</a>
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<div class="helpbox" id="hq">
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Enter query sequence in the text area. No hyphens are allowed. To determine the format of the input automatically, certain conventions are required with regard to the input of identifiers. See <a target="helpWin" title="Additional query information" href="https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=BlastHelp">Accepted Input Formats</a> for more details.
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</div>
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<textarea name="acc" cols="80" rows="10" spellcheck="false" id="id_acc">
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</textarea>
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</div>
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<!--div class="field">
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<label for="id_upload">or, upload file:</label>
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</div-->
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<div class="field">
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<a class="helplink jig-ncbitoggler ui-ncbitoggler" data-ncbitoggler-toggles="hrange" title="Sequence subrange help" href="#" id="Help_subrange">
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<span>[?]</span>
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</a>
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<div class="helpbox" id="hrange">
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Enter coordinates for a subrange of the query sequence. The ORF search will apply only to the residues in the range. Sequence coordinates are from 1 to the sequence length. The range includes the residue at the <b>To</b> coordinate.
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</div>
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<label for="id_orffrom">From:</label>
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<input type="number" name="orffrom" id="id_orffrom">
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<label for="id_orfto">To:</label>
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<input type="number" name="orfto" id="id_orfto">
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</div>
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</fieldset>
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<fieldset>
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<legend>Choose Search Parameters</legend>
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<div class="field">
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<label for="id_minlen">Minimal ORF length (nt):</label>
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<select name="minlen" id="id_minlen">
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<option value="10">30</option>
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<option value="25" selected>75</option>
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<option value="50">150</option>
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<option value="100">300</option>
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<option value="200">600</option>
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</select>
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<a class="helplink jig-ncbitoggler ui-ncbitoggler" data-ncbitoggler-toggles="hminlen" title="Minimal ORF length help" href="#" id="Help_minlen">
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<span>[?]</span>
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</a>
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<div class="helpbox" id="hminlen">
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The search will be restricted to the ORFs with the length equal or more than the selected value
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</div>
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</div>
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<div class="field">
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<label for="id_gcode">Genetic code:</label>
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<select name="gcode" id="id_gcode">
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<option value="1" selected>1. Standard</option>
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<option value="2">2. Vertebrate Mitochondrial</option>
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<option value="3">3. Yeast Mitochondrial</option>
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<option value="4">4. Mold, Protozoan and Coelenterate Mitochondrial, and the Mycoplasma/Spiroplasma</option>
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<option value="5">5. Invertebrate Mitochondrial</option>
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<option value="6">6. Ciliate, Dasycladacean and Hexamita Nuclear</option>
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<option value="9">9. Echinoderm and Flatworm Mitochondrial</option>
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<option value="10">10. Euplotid Nuclear</option>
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<option value="11">11. Bacterial, Archaeal and Plant Plastid</option>
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<option value="12">12. Alternative Yeast Nuclear</option>
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<option value="13">13. Ascidian Mitochondrial</option>
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<option value="14">14. Alternative Flatworm Mitochondrial</option>
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<option value="15">15. Blepharisma Nuclear Code</option>
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<option value="16">16. Chlorophycean Mitochondrial</option>
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<option value="21">21. Trematode Mitochondrial</option>
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<option value="22">22. Scenedesmus obliquus Mitochondrial</option>
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<option value="23">23. Thraustochytrium Mitochondrial</option>
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<option value="24">24. Pterobranchia Mitochondrial</option>
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<option value="25">25. Candidate Division SR1 and Gracilibacteria</option>
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<option value="26">26. Pachysolen tannophilus Nuclear</option>
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<option value="27">27. Karyorelict Nuclear</option>
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<option value="28">28. Condylostoma Nuclear</option>
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<option value="29">29. Mesodinium Nuclear</option>
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<option value="30">30. Peritrich Nuclear</option>
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<option value="31">31. Blastocrithidia Nuclear</option>
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<option value="33">33. Cephalodiscidae Mitochondrial UAA-Tyr Code</option>
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</select>
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<a class="helplink jig-ncbitoggler ui-ncbitoggler" data-ncbitoggler-toggles="hgcode" title="The Genetic Codes help" href="#" id="Help_gcode">
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<span>[?]</span>
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</a>
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<div class="helpbox" id="hgcode">
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The Genetic Codes are described <a target="helpWin" href="https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=c" title="The Genetic Codes">here</a>
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</div>
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</div>
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<div class="field">
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<label for="id_startcdn">ORF start codon to use:</label>
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<a class="helplink jig-ncbitoggler ui-ncbitoggler" data-ncbitoggler-toggles="hstartcdn" title="ORF start codon help" href="#" id="Help_startcdn">
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<span>[?]</span>
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</a>
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<div class="helpbox" id="hstartcdn">
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Use 'ATG' only as ORF start codon, or all alternative start codons, corresponding to the selected genetic code, or any sense codon (find all stop-to-stop ORFs)
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</div>
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<div id="id_startcdn"><div>
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<label for="id_startcdn_0"><input type="radio" name="startcdn" value="1" id="id_startcdn_0" checked>
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"ATG" only</label>
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</div><div>
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<label for="id_startcdn_1"><input type="radio" name="startcdn" value="2" id="id_startcdn_1">
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"ATG" and alternative initiation codons</label>
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</div><div>
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<label for="id_startcdn_2"><input type="radio" name="startcdn" value="3" id="id_startcdn_2">
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Any sense codon</label>
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</div>
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</div>
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</div>
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<div class="field">
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<label for="id_nested">Ignore nested ORFs:</label>
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<input type="checkbox" name="nested" id="id_nested">
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<a class="helplink jig-ncbitoggler ui-ncbitoggler" data-ncbitoggler-toggles="hnested" title="Ignore nested ORFs help" href="#" id="Help_nested">
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<span>[?]</span>
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</a>
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<div class="helpbox" id="hnested">
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If checked - ignore the ORFs completely placed within another
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</div>
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</div>
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</fieldset>
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<fieldset>
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<legend>Start Search / Clear</legend>
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<div id="buttons">
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<span><input type="submit" value="Submit" id="button_submit" class="fontgrey" disabled /></span>
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<span><input type="reset" value="Clear" id="button_clear"/></span>
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</div>
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</fieldset>
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</form>
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</div>
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</div>
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