Mercurial > repos > ktnyt > gembassy
diff GEMBASSY-1.0.3/doc/html/genret.html @ 0:8300eb051bea draft
Initial upload
| author | ktnyt |
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| date | Fri, 26 Jun 2015 05:19:29 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/GEMBASSY-1.0.3/doc/html/genret.html Fri Jun 26 05:19:29 2015 -0400 @@ -0,0 +1,17 @@ +<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" + "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd"> +<html xmlns='http://www.w3.org/1999/xhtml' xml:lang='en' lang='en'> + <head> + <title>EMBOSS: genret manual</title> + <link rel='stylesheet' type='text/css' href='/gembassy/emboss_explorer/style/emboss.css' /> + + </head> + <body> + <div id='manual'> + <!-- tfm output starts here --> + <table align=center border=0 cellspacing=0 cellpadding=0> <tr><td valign=top> <A HREF="/" ONMOUSEOVER="self.status='Go to the EMBOSS home page';return true"><img border=0 src="/gembassy/emboss_explorer/manual/emboss_icon.jpg" alt="" width=150 height=48></a> </td> <td align=left valign=middle> <b><font size="+6"> genret </font></b> </td></tr> </table> <br> <p> <!--END OF HEADER--> <H2> Function </H2> Retrieves various gene related information from genome flatfile <!-- DON'T WRITE ANYTHING HERE. IT IS DONE FOR YOU. --> <H2>Description</H2> <p> genret reads in one or more genome flatfiles and retrieves various data from<br /> the input file. It is a wrapper program to the G-language REST service,<br /> where a method is specified by giving a string to the "method" qualifier. By<br /> default, genret will parse the input file to retrieve the accession ID<br /> (or name) of the genome to query G-language REST service. By setting the<br /> "accid" qualifier to false (or 0), genret will instead parse the sequence<br /> and features of the genome to create a GenBank formatted flatfile and upload<br /> the file to the G-language web server. Using the file uploaded, genret will<br /> execute the method provided.<br /> <br /> genret is able to perform a variety of tasks, incluing the retrieval of<br /> sequence upstream, downstream, or around the start or stop codon,<br /> translated gene sequences search of gene data by keyword.<br /> <br /> Details on G-language REST service is available from the wiki page<br /> <br /> http://www.g-language.org/wiki/rest<br /> <br /> Documentation on G-language Genome Analysis Environment methods are<br /> provided at the Document Center<br /> <br /> http://ws.g-language.org/gdoc/<br /> <br /> </p> <H2>Usage</H2> Here is a sample session with genret<br><br> Retrieving sequences upstream, downstream, or around the start/stop codons. The following example shows the retrieval of sequence around the start codons of all genes.<br><br> Genes to access are specified by regular expression. '*' stands for every gene.<br><br> Available methods are:<br> after_startcodon<br> after_stopcodon<br> around_startcodon<br> around_stopcodon<br> before_startcodon<br> before_stopcodon<br><br> <table width="90%"><tr><td bgcolor="#CCFFFF"><pre> % genret Retrieves various gene related information from genome flatfile Input nucleotide sequence(s): refseqn:NC_000913 Gene name(s) to lookup [*]: Feature to access: around_startcodon Full text output file [nc_000913.around_startcodon]: </pre></td></tr></table> Go to the <a href="#input">input files</a> for this example<br> Go to the <a href="#output">output files</a> for this example<br><br> Example 2<br><br> Using flat text as target genes. The names can be split with with a space, comma, or vertical bar.<br><br> <table width="90%"><tr><td bgcolor="#CCFFFF"><pre> % genret Retrieves various gene related information from genome flatfile Input nucleotide sequence(s): refseqn:NC_000913 List of gene name(s) to report [*]: recA,recB Name of gene feature to access: translation Sequence output file [nc_000913.translation.genret]: stdout >recA MAIDENKQKALAAALGQIEKQFGKGSIMRLGEDRSMDVETISTGSLSLDIALGAGGLPMGR IVEIYGPESSGKTTLTLQVIAAAQREGKTCAFIDAEHALDPIYARKLGVDIDNLLCSQPDT GEQALEICDALARSGAVDVIVVDSVAALTPKAEIEGEIGDSHMGLAARMMSQAMRKLAGNL KQSNTLLIFINQIRMKIGVMFGNPETTTGGNALKFYASVRLDIRRIGAVKEGENVVGSETR VKVVKNKIAAPFKQAEFQILYGEGINFYGELVDLGVKEKLIEKAGAWYSYKGEKIGQGKAN ATAWLKDNPETAKEIEKKVRELLLSNPNSTPDFSVDDSEGVAETNEDF >recB MSDVAETLDPLRLPLQGERLIEASAGTGKTFTIAALYLRLLLGLGGSAAFPRPLTVEELLV VTFTEAATAELRGRIRSNIHELRIACLRETTDNPLYERLLEEIDDKAQAAQWLLLAERQMD EAAVFTIHGFCQRMLNLNAFESGMLFEQQLIEDESLLRYQACADFWRRHCYPLPREIAQVV FETWKGPQALLRDINRYLQGEAPVIKAPPPDDETLASRHAQIVARIDTVKQQWRDAVGELD ALIESSGIDRRKFNRSNQAKWIDKISAWAEEETNSYQLPESLEKFSQRFLEDRTKAGGETP RHPLFEAIDQLLAEPLSIRDLVITRALAEIRETVAREKRRRGELGFDDMLSRLDSALRSES GEVLAAAIRTRFPVAMIDEFQDTDPQQYRIFRRIWHHQPETALLLIGDPKQAIYAFRGADI FTYMKARSEVHAHYTLDTNWRSAPGMVNSVNKLFSQTDDAFMFREIPFIPVKSAGKNQALR FVFKGETQPAMKMWLMEGESCGVGDYQSTMAQVCAAQIRDWLQAGQRGEALLMNGDDARPV RASDISVLVRSRQEAAQVRDALTLLEIPSVYLSNRDSVFETLEAQEMLWLLQAVMTPEREN TLRSALATSMMGLNALDIETLNNDEHAWDVVVEEFDGYRQIWRKRGVMPMLRALMSARNIA ENLLATAGGERRLTDILHISELLQEAGTQLESEHALVRWLSQHILEPDSNASSQQMRLESD KHLVQIVTIHKSKGLEYPLVWLPFITNFRVQEQAFYHDRHSFEAVLDLNAAPESVDLAEAE RLAEDLRLLYVALTRSVWHCSLGVAPLVRRRGDKKGDTDVHQSALGRLLQKGEPQDAAGLR TCIEALCDDDIAWQTAQTGDNQPWQVNDVSTAELNAKTLQRLPGDNWRVTSYSGLQQRGHG IAQDLMPRLDVDAAGVASVVEEPTLTPHQFPRGASPGTFLHSLFEDLDFTQPVDPNWVREK LELGGFESQWEPVLTEWITAVLQAPLNETGVSLSQLSARNKQVEMEFYLPISEPLIASQLD TLIRQFDPLSAGCPPLEFMQVRGMLKGFIDLVFRHEGRYYLLDYKSNWLGEDSSAYTQQAM AAAMQAHRYDLQYQLYTLALHRYLRHRIADYDYEHHFGGVIYLFLRGVDKEHPQQGIYTTR PNAGLIALMDEMFAGMTLEEA </pre></td></tr></table> Go to the <a href="#input">input files</a> for this example<br> Go to the <a href="#output">output files</a> for this example<br><br> Example 3<br><br> Using a file with a list of gene names. The following example will retrieve the strand direction for each gene listed in the "gene_list.txt" file. String prefixed with an "@" or "list::" will be interpreted as file names.<br><br> <table width="90%"><tr><td bgcolor="#CCFFFF"><pre> % genret Retrieves various gene features from genome flatfile Input nucleotide sequence(s): refseqn:NC_000913 List of gene name(s) to report [*]: @gene_list.txt Name of gene feature to access: direction Full text output file [nc_000913.direction]: stdout gene,direction thrA,direct thrB,direct thrC,direct </pre></td></tr></table> Example 4<br><br> Retrieving translations of coding sequences.<br> The following example will retrieve the translated protein sequence of the "recA" gene.<br><br> <table width="90%"><tr><td bgcolor="#CCFFFF"><pre> % genret Retrieves various gene related information from genome flatfile Input nucleotide sequence(s): refseqn:NC_000913 Gene name(s) to lookup [*]: recA Feature to access: translation Full text output file [nc_000913.translation]: stdout >recA MAIDENKQKALAAALGQIEKQFGKGSIMRLGEDRSMDVETISTGSLSLDIALGAGGLPMGR IVEIYGPESSGKTTLTLQVIAAAQREGKTCAFIDAEHALDPIYARKLGVDIDNLLCSQPDT GEQALEICDALARSGAVDVIVVDSVAALTPKAEIEGEIGDSHMGLAARMMSQAMRKLAGNL KQSNTLLIFINQIRMKIGVMFGNPETTTGGNALKFYASVRLDIRRIGAVKEGENVVGSETR VKVVKNKIAAPFKQAEFQILYGEGINFYGELVDLGVKEKLIEKAGAWYSYKGEKIGQGKAN ATAWLKDNPETAKEIEKKVRELLLSNPNSTPDFSVDDSEGVAETNEDF </pre></td></tr></table> Go to the <a href="#input">input files</a> for this example<br> Go to the <a href="#output">output files</a> for this example<br><br> Example 5<br><br> Retrieving feature information of the genes.<br> The following example will retrieve the start positions for each gene. The values for the keys in GenBank format is available for retrieval. (ex. start end direction GO* etc.)<br> Positions will be returned with a 1 start value.<br><br> <table width="90%"><tr><td bgcolor="#CCFFFF"><pre> % genret Retrieves various gene related information from genome flatfile Input nucleotide sequence(s): refseqn:NC_000913 Gene name(s) to lookup [*]: Feature to access: start Full text output file [nc_000913.start]: </pre></td></tr></table> Go to the <a href="#input">input files</a> for this example<br> Go to the <a href="#output">output files</a> for this example<br><br> Example 6<br><br> Passing extra arguments to the methods.<br> The following example shows the retrieval of 30 base pairs around the start codon of the "recA" gene. By default, the "around_startcodon" method returns 200 base pairs around the start codon. Using the "-argument" qualifier allows the user to change this value.<br><br> <table width="90%"><tr><td bgcolor="#CCFFFF"><pre> % genret refseqn:NC_000913 recA around_startcodon -argument 30,30 stdout Retrieves various gene features from genome flatfile >recA ccggtattacccggcatgacaggagtaaaaatggctatcgacgaaaacaaacagaaagcgt tg </pre></td></tr></table> Go to the <a href="#input">input files</a> for this example<br> Go to the <a href="#output">output files</a> for this example<br><br> Example 7<br><br> Re-annotating a flatfile. genret supports re-annotation of a genome flatfile via Restauro-G service developed by our team. The original software is available at [<a href="http://restauro-g.iab.keio.ac.jp/">http://restauro-g.iab.keio.ac.jp</a>].<br><br> <table width="90%"><tr><td bgcolor="#CCFFFF"><pre> % genret refseqn:NC_000913 '*' annotate nc_000913-annotate.gbk Retrieves various gene features from genome flatfile </pre></td></tr></table> Go to the <a href="#input">input files</a> for this example<br> Go to the <a href="#output">output files</a> for this example<br><br> <h2>Command line arguments</h2> <table border cellspacing=0 cellpadding=3 bgcolor="#ccccff"> <tr bgcolor="#FFFFCC"> <th align="left">Qualifier</th> <th align="left">Type</th> <th align="left">Description</th> <th align="left">Allowed values</th> <th align="left">Default</th> </tr> <tr bgcolor="#FFFFCC"> <th align="left" colspan=5>Standard (Mandatory) qualifiers</th> </tr> <tr bgcolor="#FFFFCC"> <td>[-sequence]<br>(Parameter 1)</td> <td>seqall</td> <td>Nucleotide sequence(s) filename and optional format, or reference (input USA)</td> <td>Readable sequence(s)</td> <td><b>Required</b></td> </tr> <tr bgcolor="#FFFFCC"> <td>[-gene]<br>(Parameter 2)</td> <td>string</td> <td>List of gene name(s) to report</td> <td>Any string</td> <td>*</td> </tr> <tr bgcolor="#FFFFCC"> <td>[-access]<br>(Parameter 3)</td> <td>string</td> <td>Name of gene feature to access</td> <td>Any word</td> <td> </td> </tr> <tr bgcolor="#FFFFCC"> <td>[-outfile]<br>(Parameter 4)</td> <td>outfile</td> <td>Sequence output file</td> <td>Output file</td> <td><i><*></i>.genret</td> </tr> <tr bgcolor="#FFFFCC"> <th align="left" colspan=5>Additional (Optional) qualifiers</th> </tr> <tr> <td colspan=5>(none)</td> </tr> <tr bgcolor="#FFFFCC"> <th align="left" colspan=5>Advanced (Unprompted) qualifiers</th> </tr> <tr bgcolor="#FFFFCC"> <td>-argument</td> <td>string</td> <td>Extra arguments to pass to method</td> <td>Any string</td> <td> </td> </tr> <tr bgcolor="#FFFFCC"> <td>-[no]accid</td> <td>boolean</td> <td>Include to use sequence accession ID as query</td> <td>Boolean value Yes/No</td> <td>Yes</td> </tr> </table> <h2 id="input">Input file format</h2> <p> Database definitions for the examples are included in the embossrc_template<br /> file of the Keio Bioinformatcs Web Service (KBWS) package.<br /> <br /> Input files for usage example 4<br /> <br /> File: gene_list.txt<br /> <br /> thrA<br /> thrB<br /> thrC<br /> <br /> </p> <h2 id="output">Output file format</h2> <p> Output files for usage example 1<br /> <br /> File: nc_000913.around_startcodon<br /> <br /> <table width="90%"><tr><td bgcolor="#CCFFCC"> >thrL<br /> cgtgagtaaattaaaattttattgacttaggtcactaaatactttaaccaatataggcata<br /> gcgcacagacagataaaaattacagagtacacaacatccatgaaacgcattagcaccacca<br /> ttaccaccaccatcaccattaccacaggtaacggtgcgggctgacgcgtacaggaaacaca<br /> gaaaaaagcccgcacctgac<br /> >thrA<br /> aggtaacggtgcgggctgacgcgtacaggaaacacagaaaaaagcccgcacctgacagtgc<br /> gggctttttttttcgaccaaaggtaacgaggtaacaaccatgcgagtgttgaagttcggcg<br /> gtacatcagtggcaaatgcagaacgttttctgcgtgttgccgatattctggaaagcaatgc<br /> caggcaggggcaggtggcca<br /> <br /> <font color=red>[Part of this file has been deleted for brevity]</font><br /> <br /> >yjjY<br /> tgcatgtttgctacctaaattgccaactaaatcgaaacaggaagtacaaaagtccctgacc<br /> tgcctgatgcatgctgcaaattaacatgatcggcgtaacatgactaaagtacgtaattgcg<br /> ttcttgatgcactttccatcaacgtcaacaacatcattagcttggtcgtgggtactttccc<br /> tcaggacccgacagtgtcaa<br /> >yjtD<br /> tttttctgcgacttacgttaagaatttgtaaattcgcaccgcgtaataagttgacagtgat<br /> cacccggttcgcggttatttgatcaagaagagtggcaatatgcgtataacgattattctgg<br /> tcgcacccgccagagcagaaaatattggggcagcggcgcgggcaatgaaaacgatggggtt<br /> tagcgatctgcggattgtcg<br /> </td></tr></table> <br /> Output files for usage example 3<br /> <br /> File: nc_000913.start<br /> <br /> <table width="90%"><tr><td bgcolor="#CCFFCC"> gene,start<br /> thrL,190<br /> thrA,337<br /> thrB,2801<br /> thrC,3734<br /> yaaX,5234<br /> yaaA,5683<br /> yaaJ,6529<br /> talB,8238<br /> mog,9306<br /> <br /> <font color=red>[Part of this file has been deleted for brevity]</font><br /> <br /> yjjX,4631256<br /> ytjC,4631820<br /> rob,4632464<br /> creA,4633544<br /> creB,4634030<br /> creC,4634719<br /> creD,4636201<br /> arcA,4637613<br /> yjjY,4638425<br /> yjtD,4638965<br /> </td></tr></table><br /> Output files for usage example 7<br /> <br /> File: ecoli-annotate.gbk<br /> <br /> <table width="90%"><tr><td bgcolor="#CCFFCC"> LOCUS NC_000913 4639675 bp DNA circular BCT 25-OCT-2010<br /> DEFINITION Escherichia coli str. K-12 substr. MG1655 chromosome, complete<br /> genome.<br /> ACCESSION NC_000913<br /> VERSION NC_000913.2 GI:49175990<br /> DBLINK Project: 57779<br /> KEYWORDS .<br /> SOURCE Escherichia coli str. K-12 substr. MG1655<br /> ORGANISM Escherichia coli str. K-12 substr. MG1655<br /> Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales;<br /> <br /> <font color="red">[Part of this file has been deleted for brevity]</font><br /> <br /> CDS 2801..3733<br /> /EC_number="2.7.1.39"<br /> /codon_start="1"<br /> /db_xref="GI:16127997"<br /> /db_xref="ASAP:ABE-0000010"<br /> /db_xref="UniProtKB/Swiss-Prot:P00547"<br /> /db_xref="ECOCYC:EG10999"<br /> /db_xref="EcoGene:EG10999"<br /> /db_xref="GeneID:947498"<br /> /function="enzyme; Amino acid biosynthesis: Threonine"<br /> /function="1.5.1.8 metabolism; building block<br /> biosynthesis; amino acids; threonine"<br /> /function="7.1 location of gene products; cytoplasm"<br /> /gene="thrB"<br /> /gene_synonym="ECK0003; JW0002"<br /> /locus_tag="b0003"<br /> /note="GO_component: GO:0005737 - cytoplasm; GO_process:<br /> GO:0009088 - threonine biosynthetic process"<br /> /product="homoserine kinase"<br /> /protein_id="NP_414544.1"<br /> /rs_com="FUNCTION: Catalyzes the ATP-dependent<br /> phosphorylation of L- homoserine to L-homoserine<br /> phosphate (By similarity)."<br /> /rs_com="CATALYTIC ACTIVITY: ATP + L-homoserine = ADP +<br /> O-phospho-L- homoserine."<br /> /rs_com="PATHWAY: Amino-acid biosynthesis; L-threonine<br /> biosynthesis; L- threonine from L-aspartate: step 4/5."<br /> /rs_com="SUBCELLULAR LOCATION: Cytoplasm (Potential)."<br /> /rs_com="SIMILARITY: Belongs to the GHMP kinase family.<br /> Homoserine kinase subfamily."<br /> /rs_des="RecName: Full=Homoserine kinase; Short=HK;<br /> Short=HSK; EC=2.7.1.39;"<br /> /rs_protein="Level 1: similar to KHSE_ECODH 1.7e-180"<br /> /rs_xr="EMBL; CP000948; ACB01208.1; -; Genomic_DNA."<br /> /rs_xr="RefSeq; YP_001728986.1; -."<br /> /rs_xr="ProteinModelPortal; B1XBC8; -."<br /> /rs_xr="SMR; B1XBC8; 2-308."<br /> /rs_xr="EnsemblBacteria; EBESCT00000012034;<br /> EBESCP00000011562; EBESCG00000011096."<br /> /rs_xr="GeneID; 6058639; -."<br /> /rs_xr="GenomeReviews; CP000948_GR; ECDH10B_0003."<br /> /rs_xr="KEGG; ecd:ECDH10B_0003; -."<br /> /rs_xr="HOGENOM; HBG646290; -."<br /> /rs_xr="OMA; GSAHADN; -."<br /> /rs_xr="ProtClustDB; PRK01212; -."<br /> /rs_xr="BioCyc; ECOL316385:ECDH10B_0003-MONOMER; -."<br /> /rs_xr="GO; GO:0005737; C:cytoplasm;<br /> IEA:UniProtKB-SubCell."<br /> /rs_xr="GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW."<br /> /rs_xr="GO; GO:0004413; F:homoserine kinase activity;<br /> IEA:EC."<br /> /rs_xr="GO; GO:0009088; P:threonine biosynthetic process;<br /> IEA:UniProtKB-KW."<br /> /rs_xr="HAMAP; MF_00384; Homoser_kinase; 1; -."<br /> /rs_xr="InterPro; IPR006204; GHMP_kinase."<br /> /rs_xr="InterPro; IPR013750; GHMP_kinase_C."<br /> /rs_xr="InterPro; IPR006203; GHMP_knse_ATP-bd_CS."<br /> /rs_xr="InterPro; IPR000870; Homoserine_kin."<br /> /rs_xr="InterPro; IPR020568; Ribosomal_S5_D2-typ_fold."<br /> /rs_xr="InterPro; IPR014721;<br /> Ribosomal_S5_D2-typ_fold_subgr."<br /> /rs_xr="Gene3D; G3DSA:3.30.230.10;<br /> Ribosomal_S5_D2-type_fold; 1."<br /> /rs_xr="Pfam; PF08544; GHMP_kinases_C; 1."<br /> /rs_xr="Pfam; PF00288; GHMP_kinases_N; 1."<br /> /rs_xr="PIRSF; PIRSF000676; Homoser_kin; 1."<br /> /rs_xr="PRINTS; PR00958; HOMSERKINASE."<br /> /rs_xr="SUPFAM; SSF54211; Ribosomal_S5_D2-typ_fold; 1."<br /> /rs_xr="TIGRFAMs; TIGR00191; thrB; 1."<br /> /rs_xr="PROSITE; PS00627; GHMP_KINASES_ATP; 1."<br /> /transl_table="11"<br /> /translation="MVKVYAPASSANMSVGFDVLGAAVTPVDGALLGDVVTVEAAETF<br /> SLNNLGRFADKLPSEPRENIVYQCWERFCQELGKQIPVAMTLEKNMPIGSGLGSSACS<br /> VVAALMAMNEHCGKPLNDTRLLALMGELEGRISGSIHYDNVAPCFLGGMQLMIEENDI<br /> ISQQVPGFDEWLWVLAYPGIKVSTAEARAILPAQYRRQDCIAHGRHLAGFIHACYSRQ<br /> PELAAKLMKDVIAEPYRERLLPGFRQARQAVAEIGAVASGISGSGPTLFALCDKPETA<br /> QRVADWLGKNYLQNQEGFVHICRLDTAGARVLEN"<br /> <br /> <font color="red">[Part of this file has been deleted for brevity]</font><br /> <br /> 4639201 gcgcagtcgg gcgaaatatc attactacgc cacgccagtt gaactggtgc cgctgttaga<br /> 4639261 ggaaaaatct tcatggatga gccatgccgc gctggtgttt ggtcgcgaag attccgggtt<br /> 4639321 gactaacgaa gagttagcgt tggctgacgt tcttactggt gtgccgatgg tggcggatta<br /> 4639381 tccttcgctc aatctggggc aggcggtgat ggtctattgc tatcaattag caacattaat<br /> 4639441 acaacaaccg gcgaaaagtg atgcaacggc agaccaacat caactgcaag ctttacgcga<br /> 4639501 acgagccatg acattgctga cgactctggc agtggcagat gacataaaac tggtcgactg<br /> 4639561 gttacaacaa cgcctggggc ttttagagca acgagacacg gcaatgttgc accgtttgct<br /> 4639621 gcatgatatt gaaaaaaata tcaccaaata aaaaacgcct tagtaagtat ttttc<br /> //<br /> </td></tr></table> </p> <h2>Data files</h2> <p> None. </p> <h2>Notes</h2> <p> None. </p> <h2>References</h2> <pre> Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306. Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for large-scale analysis of high-throughput omics data, J. Pest Sci., 31, 7. Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome Analysis Environment with REST and SOAP Web Service Interfaces, Nucleic Acids Res., 38, W700-W705. </pre> <h2>Warnings</h2> <p> None. </p> <h2>Diagnostic Error Messages</h2> <p> None. </p> <h2>Exit status</h2> <p> It always exits with a status of 0. </p> <h2>Known bugs</h2> <p> None. </p> <h2>See also</h2> <table border cellpadding=4 bgcolor="#FFFFF0"><tr><th>Program name</th> <th>Description</th></tr> <tr> <td><a href="entret">entret</a></td> <td>Retrieve sequence entries from flatfile databases and files</td> </tr><tr> <td><a href="seqret">seqret</a></td> <td>Read and write (return) sequences</td> </tr> </table> <h2>Author(s)</h2> <pre> Hidetoshi Itaya (celery@g-language.org) Institute for Advanced Biosciences, Keio University 252-0882 Japan Kazuharu Arakawa (gaou@sfc.keio.ac.jp) Institute for Advanced Biosciences, Keio University 252-0882 Japan</pre> <h2>History</h2> 2012 - Written by Hidetoshi Itaya <h2>Target users</h2> This program is intended to be used by everyone and everything, from naive users to embedded scrips. <h2>Comments</h2> None. </HTML> + + <!-- tfm output ends here --> + </div> + </body> +</html>