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Sequence Similarity Search - BLAST
<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd"> <html> <head> <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1"> <meta http-equiv="Content-Style-Type" content="text/css"> <meta http-equiv="Content-Script-Type" content="text/javascript"> <title>Sequence Similarity Search - BLAST</title> <link rel="stylesheet" href="/css/gn2.css?20180209" type="text/css"> <script src="/js/align.js?20180209" type="text/javascript"></script> </head> <body bgcolor="#ffffff" link="#003399" vlink="#003399" onLoad="init()"> <table width=680> <tr> <td width=180 align="center"> <a href="https://www.genome.jp/"><img src="/Fig/gntop2.gif" alt="GenomeNet icon" border=0></a> </td> <td> <h2 class="title2">BLAST Search</h2> </td> </tr> </table> <br> <table width=680 cellpadding=2 class="frame2"> <tr><td align="center" class="td20"> <table width=660> <tr> <th><font class="current">BLAST</font></th> <th><a href="/tools/fasta/">FASTA</a></th> <th><a href="https://www.genome.jp/kegg/kegg2.html">KEGG2</a></th> </tr> </table> </td></tr> <tr><td> <!-- start --> <br><div style="margin-left:20px"> <table width=640> <tr><td> <form name="blast" method="post" action="/tools-bin/blastplus" enctype="multipart/form-data"> <table width=620><tr><td align=right> <input type=submit value="Compute"> <input type=reset value="Clear" onClick="formClear(this.form)"> </td></tr></table> <b>Enter query sequence:</b> (in one of the three forms)<br><br> <table> <tr valign="top"><td>Sequence ID</td> <td><input type="text" name="seqid" size=20> (Example) mja:MJ_1041</td></tr> <tr valign="top"><td>Local file name</td> <td><input type="file" name="upload_file" size=30></td></tr> <tr valign="top"><td>Sequence data</td> <td><textarea name="sequence" cols="60" rows="5"></textarea></td></tr> </table> <br> <b>Select program and database:</b><br><br> <table> <tr valign="top"> <td><input type="radio" name="prog" value="blastp" onClick="set_dbtype(this.form,'prot')" checked> BLASTP (prot query vs prot db)<br> <input type="radio" name="prog" value="blastx" onClick="set_dbtype(this.form,'prot')"> BLASTX (nucl query vs prot db)</td> <td> <table width=360 border=1 cellpadding=0 cellspacing=0><tr><td> <input type="radio" name="dbname" value="genes" checked> KEGG GENES<br> <table border=0 cellpadding=0 cellspacing=0> <tr><td> <input type="radio" name="dbname" value="eukaryotes"></td><td> Eukaryotes <input type="radio" name="dbname" value="prokaryotes"> Prokaryotes <input type="radio" name="dbname" value="T40000.pep"> Viruses</td></tr> <tr><td> <input type="radio" name="dbname" value="mine-aa"></td><td> Favorite <a href="https://www.genome.jp/kegg/catalog/org_list.html">organism code or category</a><br> </td></tr><tr><td> </td><td> <input type="text" name="myspecies-aa" id="myspecies-aa" placeholder="hsa ptr ggo" size=30 onFocus="set_mysp(this.form,'mine-aa')"><br> </td></tr> </table> <input type="radio" name="dbname" value="mgenes"> KEGG MGENES<br> <table border=0 cellpadding=0 cellspacing=0> <tr><td> <input type="radio" name="dbname" value="environmental"></td><td> Environmental <input type="radio" name="dbname" value="organismal"> Organismal</td></tr> <tr><td> <input type="radio" name="dbname" value="mine-samples-aa"></td><td> Favorite <a href="https://www.genome.jp/kegg/catalog/org_list3.html">samples</a><br> </td></tr><tr><td> </td><td> <input type="text" name="mysamples-aa" id="mysamples-aa" placeholder="Gut T30143" size=30 onFocus="set_mysp(this.form,'mine-samples-aa')"><br> </td></tr> </table> <input type="radio" name="dbname" value="refgene"> Microbial Reference Genes<br> <table border=0 cellpadding=0 cellspacing=0> <tr><td> <input type="radio" name="dbname" value="RG001.pep"></td><td> Ocean (OM-RGC) <input type="radio" name="dbname" value="RG002.pep"> Human gut (IGC)</td></tr> <!-- <tr><td> <input type="radio" name="dbname" value="mine-samples-refgene-aa"></td><td> Favorite <a href="https://www.genome.jp/kegg/catalog/org_list3.html">samples</a><br> </td></tr><tr><td> </td><td> <input type="text" name="mysamples-refgene-aa" id="mysamples-refgene-aa" size=30 onFocus="set_mysp(this.form,'mine-samples-refgene-aa')"><br> </td></tr> --> </table> <input type="radio" name="dbname" value="nr-aa"> nr-aa (GenBank, UniProt, RefSeq and PDBSTR)<br> <input type="radio" name="dbname" value="swissprot"> Swiss-Prot <input type="radio" name="dbname" value="uniprot"> UniProt <input type="radio" name="dbname" value="refpep"> RefSeq <br> <input type="radio" name="dbname" value="pdbstr"> PDBSTR <br> <input type="radio" name="dbname" value="uniref50"> UniRef50 <input type="radio" name="dbname" value="uniref90"> UniRef90 <input type="radio" name="dbname" value="uniref100"> UniRef100 <br> <input type="radio" name="dbname" value="virushostdb.cds.faa"> Virus-Host DB<br> </td></tr> </table> </td> </tr> <tr valign="top"> <td><input type="radio" name="prog" value="blastn" onClick="set_dbtype(this.form,'nucl')"> BLASTN (nucl query vs nucl db)<br> <input type="radio" name="prog" value="tblastn" onClick="set_dbtype(this.form,'nucl')"> TBLASTN (prot query vs nucl db)</td> <td> <table width=360 border=1 cellpadding=0 cellspacing=0><tr><td> <input type="radio" name="dbname" value="genes-nt"> KEGG GENES<br> <table border=0 cellpadding=0 cellspacing=0> <tr><td> <input type="radio" name="dbname" value="eukaryotes-nt"></td><td> Eukaryotes <input type="radio" name="dbname" value="prokaryotes-nt"> Prokaryotes <input type="radio" name="dbname" value="T40000.nuc"> Viruses</td></tr> <tr><td> <input type="radio" name="dbname" value="mine-nt"></td><td> Favorite <a href="https://www.genome.jp/kegg/catalog/org_list.html">organism code or category</a><br> </td></tr><tr><td> </td><td> <input type="text" name="myspecies-nt" id="myspecies-nt" placeholder="hsa ptr ggo" size=30 onFocus="set_mysp(this.form,'mine-nt')"><br> </td></tr> </table> <input type="radio" name="dbname" value="mgenes-nt"> KEGG MGENES<br> <table border=0 cellpadding=0 cellspacing=0> <tr><td> <input type="radio" name="dbname" value="environmental-nt"></td><td> Environmental <input type="radio" name="dbname" value="organismal-nt"> Organismal</td></tr> <tr><td> <input type="radio" name="dbname" value="mine-samples-nt"></td><td> Favorite <a href="https://www.genome.jp/kegg/catalog/org_list3.html">samples</a><br> </td></tr><tr><td> </td><td> <input type="text" name="mysamples-nt" id="mysamples-nt" placeholder="T30798 T30799" size=30 onFocus="set_mysp(this.form,'mine-samples-nt')"><br> </td></tr> </table> <input type="radio" name="dbname" value="genome"> KEGG GENOME<br> <table border=0 cellpadding=0 cellspacing=0><tr><td> <input type="radio" name="dbname" value="mine_genome"></td><td> Favorite <a href="https://www.genome.jp/kegg/catalog/org_list.html">organism code or category</a><br> </td></tr><tr><td> </td><td> <input type="text" name="mygenome" id="mygenome" placeholder="Escherichia Salmonella" size=30 onFocus="set_mygn(this.form,'nucl')"><br> </td></tr> </table> <input type="radio" name="dbname" value="refgene-nt"> Microbial Reference Genes<br> <table border=0 cellpadding=0 cellspacing=0> <tr><td> <input type="radio" name="dbname" value="RG001.nuc"></td><td> Ocean (OM-RGC) <input type="radio" name="dbname" value="RG002.nuc"> Human gut (IGC)</td></tr> <tr><td> <input type="radio" name="dbname" value="RG003.nuc"></td><td> Ocean (MATOU)</td></tr> <!-- <tr><td> <input type="radio" name="dbname" value="mine-samples-refgene-nt"></td><td> Favorite <a href="https://www.genome.jp/kegg/catalog/org_list3.html">samples</a><br> </td></tr><tr><td> </td><td> <input type="text" name="mysamples-refgene-nt" id="mysamples-refgene-nt" size=30 onFocus="set_mysp(this.form,'mine-samples-refgene-nt')"><br> </td></tr> --> </table> <!-- <input type="radio" name="dbname" value="egenes-nt"> EGENES<br> --> <input type="radio" name="dbname" value="nr-nt"> nr-nt (GenBank, EMBL and RefSeq)<br> <input type="radio" name="dbname" value="dbest"> dbEST <input type="radio" name="dbname" value="dbgss"> dbGSS <input type="radio" name="dbname" value="htgs"> HTGs <input type="radio" name="dbname" value="dbsts"> dbSTS <br> <input type="radio" name="dbname" value="refnuc"> RefSeq <br> <input type="radio" name="dbname" value="RibosomalDB"> Ribosomal Databases <br> <input type="radio" name="dbname" value="silva_ssu"> SILVA (SSU, 16S/18S) <input type="radio" name="dbname" value="silva_lsu"> SILVA (LSU, 23S/28S) <br> <input type="radio" name="dbname" value="pr2"> PR2 (Protist Reference) <br> <input type="radio" name="dbname" value="rdp_prokaryotic"> RDP (Prokaryotic 16S) <input type="radio" name="dbname" value="rdp_fungal"> RDP (Fungal 28S) <br> <input type="radio" name="dbname" value="epd"> EPD <br> <input type="radio" name="dbname" value="virushostdb.cds.fna"> Virus-Host DB Genes<br> <input type="radio" name="dbname" value="virushostdb.genomic.fna"> Genomes <br> <input type="radio" name="dbname" value="Environmental_Viral_Genome"> Environmental Viral Genome<br>   <select multiple name="environmental_viral_genome" id="environmental_viral_genome"> <option value="Environmental_Viral_Genome"> All <option value="Aylward_2021"> Aylward 2021 <option value="Gaia_2023"> Gaia 2023 <option value="Backstrom_2019"> Backstrom 2019 <option value="Buscaglia_2024"> Buscaglia 2024 <option value="Fang_2024"> Fang 2024 <option value="Liang_2024"> Liang 2024 <option value="Minch_2024"> Minch 2024 <option value="Monir_2020"> Monir 2020 <option value="Piedade_2024"> Piedade 2024 <option value="Zhang_2024"> Zhang 2024 <option value="Schulz_2020"> Schulz 2020 </select> <br> <br> </td></tr></table> </td> </tr> </table> <br> <table> <tr valign="top"><td>Scoring matrix:</td> <td> <select name="matrix"> <option value="blosum62" selected> BLOSUM62 <option value="blosum80"> BLOSUM80 <option value="pam30"> PAM30 <option value="pam70"> PAM70 <option value="pam250"> PAM250 </select> (except for BLASTN) </td> <td> </td> <td>Filter:</td><td> <select name="filter"> <option value="F" selected> None <option value="T">DUST in BLASTN, SEG in others </select> </td></tr></table> <br> <b>Output options:</b> <br><br><div style="margin-left:30px"> Set the maximum number of database sequences to be reported: <input name="V_value" size=3 value="500" maxlength=4> <br> Set the maximum number of alignments to be displayed: <input name="B_value" size=3 value="250" maxlength=4> </div> <hr class="frame2"> <b>Optional parameters:</b> (see <a href="/tools-bin/show_man?blast2">manual</a> for details) <br><br><div style="margin-left:30px"> <table> <tr valign="top"><td>E-value threshold</td><td><input type="text" name="Evalue" size=10 value="10.0"></td></tr> <tr valign="top"><td>Alignment view:</td><td> <select name="alignment_view"> <option value=0 selected> Pairwise <option value=1> master-slave with identities <option value=2> master-slave without identities <option value=3> flat master-slave with identities <option value=4> flat master-slave without identities <option value=11> Get ASN.1 for SeqAnnot <option value=13> Get ASN.1 for the Blast Object </select> (except for BLASTX) </td></tr> <tr valign="top"><td>Additional options:</td><td> <input size=54 name="other_param"><br> (delimited by whitespaces) </td></tr> </table> </div> </form> </td></tr> </table> </div> <!-- end --> </td></tr> <tr><td align="center" class="td20"> <table width=660> <tr> <th><a href="https://www.genome.jp/feedback/?category=blastfasta">Feedback</a></th> <th><a href="https://www.genome.jp/kegg/">KEGG</a></th> <th><a href="https://www.genome.jp/">GenomeNet</a></th> <td align="center"><a href="http://www.bic.kyoto-u.ac.jp/">Kyoto University Bioinformatics Center</a></td> </tr> </table> </td></tr> </table> </body> </html>