ncbitools NCBI=/bio/mb/ncbi/ncbirc ncbipath=/bio/mb/ncbi/bin/ stderr=childapp.stderr stdout=childapp.stdout ncbitools-packinfo About/NCBI Tools TITLE NCBI Tools INFO About National Center for Biotechnology Information(NCBI) Tool Kit. Includes BLAST and related software. HELP Help http://www.ncbi.nih.gov/IEB/ToolBox/ versionDec 2001 dateThu Dec 20 11:43:53 EST 2001 reference source ftp://ncbi.nlm.nih.gov/toolbox/ncbi_tools/ncbi.tar.gz working source ftp://iubio.bio.indiana.edu/molbio/ncbi/ncbi_tools/ncbi-01dec.tar.gz blastall Database/Sequence Search/Blast All (NCBI) ${ncbipath}blastall $blastn $blastp $blastx $tblastn $tblastx $queryFile $dbName $OUTfile TITLE Blast All (NCBI) INFO About Database - Sequence Search - Blast All (NCBI) HELP Help for Blast All ${ncbipath}docs/README.bls cblastProg Program choices true blastProg false blastn blastn - nucleotide query to a nucleotide database true -p blastn blastp blastp - protein query to a protein database false -p blastp blastx blastx - nucleotide (translated) query to a protein database false -p blastx tblastn tblastn - protein query to a nucleotide (translated) database false -p tblastn tblastx tblastx - nucleotide (translated) query to a nucleotide (translated) database false -p tblastx IOFiles Input/Output files false queryFile Query File blastquery.fa input biosequence/fasta input -i $value dbName Database Name nr.fa input biosequence/fasta serverlocal -d $value OUTfile BLAST report Output File blastreport.txt output text/plain output -o $value STDOUT Command_Output output text/plain stdout ${stdout} STDERR Errors output text/plain stderr ${stderr} formatdb Database/Utilities/Format Blast Data (NCBI) ${ncbipath}formatdb $dbProt $dbNuc $dbFile $logFile TITLE Format Blast Data (NCBI) INFO About Database - Format Blast Data (NCBI) HELP Help for Format DB ${ncbipath}docs/README.formatdb c.dbtype Program choices true ch.dbtype Type of file false dbProt Protein true -p T dbNuc Nucleotide false -p F IOFiles Input/Output files false dbFile Database File blast.fa input biosequence/fasta input -i $value logFile Log File formatdb.log output text/plain output -l $value STDOUT Command_Output output text/plain stdout ${stdout} STDERR Errors output text/plain stderr ${stderr}