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.TH BLAST 1 2004-10-20 NCBI "NCBI Tools User's Manual"
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bl2seq, blast2, blastall, blastcl3, blastpgp, impala, megablast, rpsblast, seedtop \- Basic Local Alignment Search Tool
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[\|\fB\-D\fP\ \fIN\fP\|]
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[\|\fB\-E\fP\ \fIN\fP\|]
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[\|\fB\-F\fP\ \fIstr\fP\|]
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[\|\fB\-G\fP\ \fIN\fP\|]
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[\|\fB\-I\fP\ \(dq\fIstart\ stop\fP\(dq\|]
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[\|\fB\-J\fP\ \(dq\fIstart\ stop\fP\(dq\|]
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[\|\fB\-M\fP\ \fIstr\fP\|]
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[\|\fB\-S\fP\ \fIN\fP\|]
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[\|\fB\-W\fP\ \fIN\fP\|]
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[\|\fB\-X\fP\ \fIN\fP\|]
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[\|\fB\-Y\fP\ \fIX\fP\|]
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[\|\fB\-a\fP\ \fIfilename\fP\|]
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[\|\fB\-d\fP\ \fIN\fP\|]
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[\|\fB\-e\fP\ \fIX\fP\|]
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\fB\-i\fP\ \fIfilename\fP
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\fB\-j\fP\ \fIfilename\fP
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[\|\fB\-o\fP\ \fIfilename\fP\|]
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[\|\fB\-q\fP\ \fIN\fP\|]
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[\|\fB\-r\fP\ \fIN\fP\|]
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[\|\fB\-t\fP\ \fIN\fP\|]
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[\|\fB\-B\fP\ \fIN\fP\|]
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[\|\fB\-D\fP\ \fIN\fP\|]
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[\|\fB\-E\fP\ \fIN\fP\|]
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[\|\fB\-F\fP\ \fIstr\fP\|]
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[\|\fB\-G\fP\ \fIN\fP\|]
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[\|\fB\-I\fP\ \(dq\fIstart\ stop\fP\(dq\|]
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[\|\fB\-J\fP\ \(dq\fIstart\ stop\fP\(dq\|]
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[\|\fB\-M\fP\ \fIstr\fP\|]
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[\|\fB\-O\fP\ \fIfilename\fP\|]
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[\|\fB\-P\fP\ \fIX\fP\|]
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[\|\fB\-Q\fP\ \fIN\fP\|]
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[\|\fB\-R\fP\ \fIstr\fP\|]
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[\|\fB\-S\fP\ \fIN\fP\|]
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[\|\fB\-T\fP\ \fIN\fP\|]
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[\|\fB\-W\fP\ \fIN\fP\|]
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[\|\fB\-X\fP\ \fIN\fP\|]
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[\|\fB\-Y\fP\ \fIX\fP\|]
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[\|\fB\-Z\fP\ \fIN\fP\|]
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[\|\fB\-a\fP\ \fIN\fP\|]
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[\|\fB\-b\fP\ \fIN\fP\|]
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[\|\fB\-d\fP\ \fIstr\fP\|]
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[\|\fB\-e\fP\ \fIX\fP\|]
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[\|\fB\-f\fP\ \fIN\fP\|]
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[\|\fB\-g\fP\ \fIN\fP\|]
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[\|\fB\-h\fP\ \fIN\fP\|]
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[\|\fB\-i\fP\ \fIfilename\fP\|]
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[\|\fB\-j\fP\ \fIfilename\fP\|]
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[\|\fB\-k\fP\ \fIstr\fP\|]
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[\|\fB\-m\fP\ \fIN\fP\|]
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[\|\fB\-o\fP\ \fIfilename\fP\|]
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[\|\fB\-q\fP\ \fIN\fP\|]
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[\|\fB\-r\fP\ \fIN\fP\|]
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[\|\fB\-s\fP\ \fIN\fP\|]
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[\|\fB\-t\fP\ \fIN\fP\|]
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[\|\fB\-v\fP\ \fIN\fP\|]
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[\|\fB\-w\fP\ \fIN\fP\|]
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[\|\fB\-y\fP\ \fIN\fP\|]
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[\|\fB\-z\fP\ \fIN\fP\|]
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[\|\fB\-A\fP\ \fIN\fP\|]
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[\|\fB\-B\fP\ \fIN\fP\|]
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[\|\fB\-D\fP\ \fIN\fP\|]
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[\|\fB\-E\fP\ \fIN\fP\|]
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[\|\fB\-F\fP\ \fIstr\fP\|]
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[\|\fB\-G\fP\ \fIN\fP\|]
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[\|\fB\-K\fP\ \fIN\fP\|]
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[\|\fB\-L\fP\ \fIstart,stop\fP\|]
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[\|\fB\-M\fP\ \fIstr\fP\|]
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[\|\fB\-O\fP\ \fIfilename\fP\|]
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[\|\fB\-P\fP\ \fIN\fP\|]
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[\|\fB\-Q\fP\ \fIN\fP\|]
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[\|\fB\-R\fP\ \fIfilename\fP\|]
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[\|\fB\-W\fP\ \fIN\fP\|]
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[\|\fB\-X\fP\ \fIN\fP\|]
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[\|\fB\-Y\fP\ \fIX\fP\|]
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[\|\fB\-Z\fP\ \fIN\fP\|]
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[\|\fB\-a\fP\ \fIN\fP\|]
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[\|\fB\-b\fP\ \fIN\fP\|]
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[\|\fB\-d\fP\ \fIstr\fP\|]
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[\|\fB\-e\fP\ \fIX\fP\|]
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[\|\fB\-f\fP\ \fIN\fP\|]
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[\|\fB\-i\fP\ \fIfilename\fP\|]
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[\|\fB\-l\fP\ \fIstr\fP\|]
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[\|\fB\-m\fP\ \fIN\fP\|]
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[\|\fB\-o\fP\ \fIfilename\fP\|]
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[\|\fB\-q\fP\ \fIN\fP\|]
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[\|\fB\-r\fP\ \fIN\fP\|]
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[\|\fB\-t\fP\ \fIN\fP\|]
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[\|\fB\-v\fP\ \fIN\fP\|]
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[\|\fB\-w\fP\ \fIN\fP\|]
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[\|\fB\-y\fP\ \fIX\fP\|]
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[\|\fB\-z\fP\ \fIX\fP\|]
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[\|\fB\-A\fP\ \fIN\fP\|]
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[\|\fB\-D\fP\ \fIN\fP\|]
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[\|\fB\-E\fP\ \fIN\fP\|]
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[\|\fB\-F\fP\ \fIstr\fP\|]
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[\|\fB\-G\fP\ \fIN\fP\|]
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[\|\fB\-K\fP\ \fIN\fP\|]
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[\|\fB\-L\fP\ \fIstart,stop\fP\|]
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[\|\fB\-M\fP\ \fIstr\fP\|]
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[\|\fB\-O\fP\ \fIfilename\fP\|]
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[\|\fB\-Q\fP\ \fIN\fP\|]
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[\|\fB\-W\fP\ \fIN\fP\|]
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[\|\fB\-X\fP\ \fIN\fP\|]
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[\|\fB\-Y\fP\ \fIX\fP\|]
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[\|\fB\-Z\fP\ \fIN\fP\|]
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[\|\fB\-a\fP\ \fIN\fP\|]
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[\|\fB\-b\fP\ \fIN\fP\|]
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[\|\fB\-d\fP\ \fIstr\fP\|]
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[\|\fB\-e\fP\ \fIX\fP\|]
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[\|\fB\-f\fP\ \fIN\fP\|]
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[\|\fB\-i\fP\ \fIfilename\fP\|]
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[\|\fB\-m\fP\ \fIN\fP\|]
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[\|\fB\-o\fP\ \fIfilename\fP\|]
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[\|\fB\-q\fP\ \fIN\fP\|]
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[\|\fB\-r\fP\ \fIN\fP\|]
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[\|\fB\-u\fP\ \fIstr\fP\|]
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[\|\fB\-t\fP\ \fIN\fP\|]
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[\|\fB\-v\fP\ \fIN\fP\|]
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[\|\fB\-w\fP\ \fIN\fP\|]
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[\|\fB\-y\fP\ \fIX\fP\|]
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[\|\fB\-z\fP\ \fIX\fP\|]
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[\|\fB\-A\fP\ \fIN\fP\|]
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[\|\fB\-B\fP\ \fIfilename\fP\|]
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[\|\fB\-C\fP\ \fIfilename\fP\|]
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[\|\fB\-E\fP\ \fIN\fP\|]
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[\|\fB\-G\fP\ \fIN\fP\|]
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[\|\fB\-H\fP\ \fIN\fP\|]
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[\|\fB\-K\fP\ \fIN\fP\|]
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[\|\fB\-L\fP\ \fIN\fP\|]
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[\|\fB\-M\fP\ \fIstr\fP\|]
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[\|\fB\-N\fP\ \fIX\fP\|]
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[\|\fB\-O\fP\ \fIfilename\fP\|]
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[\|\fB\-P\fP\ \fIN\fP\|]
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[\|\fB\-Q\fP\ \fIfilename\fP\|]
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[\|\fB\-R\fP\ \fIfilename\fP\|]
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[\|\fB\-S\fP\ \fIN\fP\|]
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[\|\fB\-W\fP\ \fIN\fP\|]
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[\|\fB\-X\fP\ \fIN\fP\|]
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[\|\fB\-Y\fP\ \fIX\fP\|]
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[\|\fB\-Z\fP\ \fIN\fP\|]
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[\|\fB\-a\fP\ \fIN\fP\|]
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[\|\fB\-b\fP\ \fIN\fP\|]
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[\|\fB\-c\fP\ \fIN\fP\|]
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[\|\fB\-d\fP\ \fIstr\fP\|]
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[\|\fB\-e\fP\ \fIX\fP\|]
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[\|\fB\-f\fP\ \fIN\fP\|]
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[\|\fB\-h\fP\ \fIX\fP\|]
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[\|\fB\-i\fP\ \fIfilename\fP\|]
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[\|\fB\-j\fP\ \fIN\fP\|]
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[\|\fB\-k\fP\ \fIfilename\fP\|]
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[\|\fB\-l\fP\ \fIstr\fP\|]
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[\|\fB\-m\fP\ \fIN\fP\|]
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[\|\fB\-o\fP\ \fIfilename\fP\|]
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[\|\fB\-p\fP\ \fIstr\fP\|]
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[\|\fB\-q\fP\ \fIN\fP\|]
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[\|\fB\-u\fP\ \fIN\fP\|]
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[\|\fB\-v\fP\ \fIN\fP\|]
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[\|\fB\-y\fP\ \fIX\fP\|]
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[\|\fB\-z\fP\ \fIN\fP\|]
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[\|\fB\-E\fP\ \fIN\fP\|]
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[\|\fB\-F\fP\ \fIstr\fP\|]
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[\|\fB\-G\fP\ \fIN\fP\|]
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[\|\fB\-M\fP\ \fIstr\fP\|]
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[\|\fB\-O\fP\ \fIfilename\fP\|]
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[\|\fB\-P\fP\ \fIfilename\fP\|]
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[\|\fB\-a\fP\ \fIN\fP\|]
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[\|\fB\-b\fP\ \fIN\fP\|]
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[\|\fB\-c\fP\ \fIN\fP\|]
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[\|\fB\-d\fP\ \fIstr\fP\|]
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[\|\fB\-e\fP\ \fIX\fP\|]
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[\|\fB\-h\fP\ \fIX\fP\|]
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[\|\fB\-i\fP\ \fIfilename\fP\|]
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[\|\fB\-j\fP\ \fIN\fP\|]
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[\|\fB\-m\fP\ \fIN\fP\|]
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[\|\fB\-o\fP\ \fIfilename\fP\|]
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[\|\fB\-v\fP\ \fIN\fP\|]
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[\|\fB\-y\fP\ \fIX\fP\|]
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[\|\fB\-z\fP\ \fIN\fP\|]
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[\|\fB\-A\fP\ \fIN\fP\|]
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[\|\fB\-D\fP\ \fIN\fP\|]
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[\|\fB\-E\fP\ \fIN\fP\|]
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[\|\fB\-F\fP\ \fIstr\fP\|]
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[\|\fB\-G\fP\ \fIN\fP\|]
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[\|\fB\-H\fP\ \fIN\fP\|]
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[\|\fB\-L\fP\ \fIstart,stop\fP\|]
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[\|\fB\-M\fP\ \fIN\fP\|]
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[\|\fB\-N\fP\ \fIN\fP\|]
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[\|\fB\-O\fP\ \fIfilename\fP\|]
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[\|\fB\-P\fP\ \fIN\fP\|]
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[\|\fB\-Q\fP\ \fIfilename\fP\|]
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[\|\fB\-S\fP\ \fIN\fP\|]
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[\|\fB\-W\fP\ \fIN\fP\|]
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[\|\fB\-X\fP\ \fIN\fP\|]
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[\|\fB\-Z\fP\ \fIN\fP\|]
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[\|\fB\-a\fP\ \fIN\fP\|]
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[\|\fB\-b\fP\ \fIN\fP\|]
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[\|\fB\-d\fP\ \fIstr\fP\|]
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[\|\fB\-e\fP\ \fIX\fP\|]
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[\|\fB\-i\fP\ \fIfilename\fP\|]
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[\|\fB\-l\fP\ \fIstr\fP\|]
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[\|\fB\-m\fP\ \fIN\fP\|]
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[\|\fB\-o\fP\ \fIfilename\fP\|]
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[\|\fB\-p\fP\ \fIX\fP\|]
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[\|\fB\-q\fP\ \fIN\fP\|]
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[\|\fB\-r\fP\ \fIN\fP\|]
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[\|\fB\-t\fP\ \fIN\fP\|]
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[\|\fB\-s\fP\ \fIN\fP\|]
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[\|\fB\-v\fP\ \fIN\fP\|]
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[\|\fB\-y\fP\ \fIN\fP\|]
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[\|\fB\-z\fP\ \fIX\fP\|]
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[\|\fB\-F\fP\ \fIstr\fP\|]
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[\|\fB\-L\fP\ \fIstart,stop\fP\|]
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[\|\fB\-N\fP\ \fIX\fP\|]
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[\|\fB\-O\fP\ \fIfilename\fP\|]
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[\|\fB\-P\fP\ \fIN\fP\|]
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[\|\fB\-X\fP\ \fIN\fP\|]
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[\|\fB\-Y\fP\ \fIX\fP\|]
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[\|\fB\-Z\fP\ \fIN\fP\|]
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[\|\fB\-a\fP\ \fIN\fP\|]
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[\|\fB\-b\fP\ \fIN\fP\|]
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\fB\-d\fP\ \fIfilename\fP
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[\|\fB\-e\fP\ \fIX\fP\|]
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[\|\fB\-i\fP\ \fIfilename\fP\|]
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[\|\fB\-l\fP\ \fIfilename\fP\|]
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[\|\fB\-m\fP\ \fIN\fP\|]
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[\|\fB\-o\fP\ \fIfilename\fP\|]
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[\|\fB\-v\fP\ \fIN\fP\|]
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[\|\fB\-y\fP\ \fIX\fP\|]
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[\|\fB\-z\fP\ \fIN\fP\|]
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[\|\fB\-C\fP\ \fIN\fP\|]
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[\|\fB\-D\fP\ \fIN\fP\|]
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[\|\fB\-E\fP\ \fIN\fP\|]
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[\|\fB\-G\fP\ \fIN\fP\|]
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[\|\fB\-M\fP\ \fIstr\fP\|]
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[\|\fB\-O\fP\ \fIfilename\fP\|]
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[\|\fB\-S\fP\ \fIN\fP\|]
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[\|\fB\-X\fP\ \fIN\fP\|]
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[\|\fB\-b\fP\ \fIN\fP\|]
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[\|\fB\-d\fP\ \fIstr\fP\|]
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[\|\fB\-e\fP\ \fIX\fP\|]
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[\|\fB\-i\fP\ \fIfilename\fP\|]
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[\|\fB\-k\fP\ \fIfilename\fP\|]
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[\|\fB\-o\fP\ \fIfilename\fP\|]
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[\|\fB\-p\fP\ \fIstr\fP\|]
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[\|\fB\-q\fP\ \fIN\fP\|]
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[\|\fB\-r\fP\ \fIN\fP\|]
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[\|\fB\-v\fP\ \fIN\fP\|]
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This manual page documents briefly the commands \fBbl2seq\fP, \fBblast\fP,
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\fBblastall\fP, \fBblastcl3\fP, \fBblastpgp\fP, \fBimpala\fP,
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\fBmegablast\fP, \fBrpsblast\fP, and \fBseedtop\fP. These commands
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are documented together because they have a lot of common options.
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\fBbl2seq\fP performs a comparison between two sequences using either
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the blastn or blastp algorithm. Both sequences must be either
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nucleotides or proteins.
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\fBblast\fP compares a sequence against either a local database or a
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second sequence; it incorporates most of the functionality of both
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\fBbl2seq\fP and \fBblastall\fP, but uses a semi-experimental new
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\fBblastall\fP finds the best matches in a local database for a
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\fBblastcl3\fP accesses the newest NCBI BLAST search engine (version
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2.0). The software behind BLAST version 2.0 was written from scratch
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to allow BLAST to handle the new challenges posed by the sequence
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databases in the coming years. Updates to this software will continue
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\fBblastpgp\fP performs gapped blastp searches and can be used to
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perform iterative searches in psi-blast and phi-blast mode.
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\fBimpala\fP searches a database of score matrices, prepared by
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\fBcopymat\fP(1), producing BLAST-like output.
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\fBmegablast\fP uses the greedy algorithm of Webb Miller et al. for
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nucleotide sequence alignment search and concatenates many queries to
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save time spent scanning the database. This program is optimized for
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aligning sequences that differ slightly as a result of sequencing or
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other similar "errors". It is up to 10 times faster than more common
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sequence similarity programs and therefore can be used to swiftly
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compare two large sets of sequences against each other.
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\fBrpsblast\fP (Reverse PSI-BLAST) searches a query sequence against a
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database of profiles. This is the opposite of PSI-BLAST that searches
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a profile against a database of sequences, hence the 'Reverse'.
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\fBrpsblast\fP uses a BLAST-like algorithm, finding single- or
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double-word hits and then performing an ungapped extension on these
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candidate matches. If a sufficiently high-scoring ungapped alignment
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is produced, a gapped extension is performed and those (gapped)
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alignments with sufficiently low expect value are reported. This
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procedure is in contrast to IMPALA that performs a Smith-Waterman
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calculation between the query and each profile, rather than using a
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word-hit approach to identify matches that should be extended.
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\fBseedtop\fP answers two relatively simple questions:
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Given a sequence and a database of patterns, which patterns occur
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in the sequence and where?
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Given a pattern and a sequence database, which sequences contain the
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Some of these commands support multiple types of comparison, governed
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by the \fB\-p\fP ("program") flag:
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compares an amino acid query sequence against a protein sequence
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compares a nucleotide query sequence against a nucleotide sequence
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compares the six-frame conceptual translation products of a nucleotide
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query sequence (both strands) against a protein sequence database.
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For \fBbl2seq\fP, the nucleotide should be the first sequence given.
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compares a protein query sequence against a nucleotide sequence
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database dynamically translated in all six reading frames (both
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strands) using a position specific matrix created by PSI-BLAST.
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compares a protein query sequence against a nucleotide sequence
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database dynamically translated in all six reading frames (both
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strands). For \fBbl2seq\fP, the nucleotide should be the second
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compares the six-frame translations of a nucleotide query sequence
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against the six-frame translations of a nucleotide sequence database.
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A summary of options is included below.
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Input sequences in the form of accession.version
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\fB\-A\ F\fP (blast2)
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Do not use AG BLAST approach to database scanning
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\fB\-A\fP\ \fIN\fP (blastall, blastcl3, blastpgp, megablast)
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Multiple Hits window size (default is 40 for blastpgp and 0 for other
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commands, but blastall and blastcl3 interpret 0 as 40 for all programs
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but blastn and megablast)
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\fB\-B\fP\ \fIN\fP (blast2)
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Produce on-the-fly tabular output:
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just offsets and quality values
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\fB\-B\fP\ \fIN\fP (blastall)
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Number of concatenated queries, in blastn or tblastn mode
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\fB\-B\fP\ \fIfilename\fP (blastpgp)
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Input Alignment File for PSI-BLAST Restart
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\fB\-C\fP\ \fIfilename\fP (blastpgp)
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Output File for PSI-BLAST Checkpointing
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\fB\-C\fP\ \fIN\fP (seedtop)
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Score only or not (default = 1)
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\fB\-D\fP\ \fIN\fP (bl2seq)
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traditional (default)
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\fB\-D\fP\ \fIN\fP (blast2, blastall, blastcl3)
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Translate sequences in the database according to genetic code \fIN\fP
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in /usr/share/ncbi/data/gc.prt (default is 1; only applies to tblast*)
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\fB\-D\fP\ \fIN\fP (megablast)
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alignment endpoints and score (default)
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all ungapped segments endpoints,
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traditional BLAST output,
491
tab-delimited one line format
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\fB\-D\fP\ \fIN\fP (seedtop)
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Cost decline to align (default = 99999)
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\fB\-E\fP\ \fIN\fP (bl2seq)
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Extending a gap costs \fIN\fP (-1 invokes default behavior; anything
500
else can result in unreliable statistics)
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\fB\-E\fP\ \fIN\fP (blast2, blastall, blastcl3, megablast)
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Extending a gap costs \fIN\fP (zero invokes default behavior:
504
non-affine if greedy, 2 otherwise, at least for blast2)
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\fB\-E\fP\ \fIN\fP (blastpgp, impala, seedtop)
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Extending a gap costs \fIN\fP (default is 1)
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\fB\-F\fP\ \fIstr\fP (bl2seq, blast2, blastall, blastpgp, blastcl3, impala,
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Filter options for DUST or SEG; defaults to \fBT\fP for bl2seq,
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blast2, blastall, blastcl3, and megablast, and to \fBF\fP for blastpgp,
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impala, and rpsblast.
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Filter sequence with SEG.
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\fB\-G\fP\ \fIN\fP (bl2seq)
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Opening a gap costs \fIN\fP (-1 invokes default behavior; anything
520
else can result in unreliable statistics)
522
\fB\-G\fP\ \fIN\fP (blast2, blastall, blastcl3, megablast)
523
Opening a gap costs \fIN\fP (zero invokes default behavior: non-affine
524
if greedy, 5 if using dynamic programming, at least for blast2)
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\fB\-G\fP\ \fIN\fP (blastpgp, impala, seedtop)
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Opening a gap costs \fIN\fP (default is 11)
532
\fB\-H\fP\ \fIN\fP (blastpgp)
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End of required region in query (-1 indicates end of query)
536
Print help (different from usage message)
538
\fB\-H\fP\ \fIN\fP (megablast)
539
Maximal number of HSPs to save per database sequence (default is 0, unlimited)
541
\fB\-I\fP\ \(dq\fIstart\ stop\fP\(dq (bl2seq, blast2)
542
Location on first (query) sequence (applies only if file specified
543
with \fB-i\fP contains a single sequence)
545
\fB\-I\fP (blastall, blastcl3, blastpgp, impala, megablast, rpsblast, seedtop)
548
\fB\-J\fP\ \(dq\fIstart\ stop\fP\(dq (bl2seq, blast2)
549
Location on second (subject) sequence (applies only if file specified
550
with \fB-j\fP contains a single sequence)
552
\fB\-J\fP (blastall, blastcl3, blastpgp, impala, megablast, rpsblast, seedtop)
553
Believe the query defline
555
\fB\-K\fP\ \fIN\fP (blastall, blastcl3, blastpgp)
556
Number of best hits from a region to keep (off by default, if used a
557
value of 100 is recommended)
560
Use (classical Mega BLAST) lookup table with width 12
562
\fB\-L\fP\ \fIstart,stop\fP (blastall, blastcl3, megablast, rpsblast)
563
Location on query sequence (for rpsblast, only valid in blastp mode)
565
\fB\-M\fP\ \fIstr\fP (bl2seq, blast2, blastall, blastcl3, blastpgp, impala, seedtop)
566
Use matrix \fIstr\fP (default = BLOSUM62)
568
\fB\-M\fP\ \fIN\fP (megablast)
569
Maximal total length of queries for a single search (default = 20000000)
572
Show only accessions for sequence IDs in tabular output
574
\fB\-N\fP\ \fIX\fP (blastpgp, rpsblast)
575
Number of bits to trigger gapping (default = 22.0)
577
\fB\-N\fP\ \fIN\fP (megablast)
578
Type of a discontiguous word template:
590
\fB\-O\fP\ \fIfilename\fP (blast2, blastall, blastcl3, blastpgp, impala, megablast, rpsblast, seedtop)
591
Write (ASN.1) sequence alignments to \fIfilename\fP; only valid for
592
blastpgp, impala, rpsblast, and seedtop with \fB\-J\fP, and only valid
593
for megablast with \fB\-D2\fP.
595
\fB\-P\fP\ \fIX\fP (blast2)
596
Identity percentage cut-off
598
\fB\-P\fP\ \fIN\fP (blastall, blastcl3, blastpgp, rpsblast)
599
Set to 1 for single-hit mode or 0 for multiple-hit mode (default).
600
Does not apply to blastn.
602
\fB\-P\fP\ \fIfilename\fP (impala)
603
Read matrix profiles from database \fIfilename\fP
605
\fB\-P\fP\ \fIN\fP (megablast)
606
Maximal number of positions for a hash value (set to 0 [default] to ignore)
608
\fB\-Q\fP\ \fIN\fP (blast2, blastall, blastcl3)
609
Translate query according to genetic code \fIN\fP in
610
/usr/share/ncbi/data/gc.prt (default is 1)
612
\fB\-Q\fP\ \fIfilename\fP (blastpgp)
613
Output File for PSI-BLAST Matrix in ASCII
615
\fB\-Q\fP\ \fIfilename\fP (megablast)
616
Masked query output; requires \fB-D\ 2\fP
618
\fB\-R\fP\ \fIstr\fP (bl2seq)
619
Range of ordinal ids in the BLAST database to search. Format:
620
\fIoid1\ oid2\fP; \fB,\fP, \fB:\fP or \fB;\fP can also be used as
621
delimiters. Full database is searched if range not provided.
623
\fB\-R\fP\ \fIfilename\fP (blastall)
624
Read PSI-TBLASTN checkpoint file \fIfilename\fP
629
\fB\-R\fP\ \fIfilename\fP (blastpgp)
630
Input File for PSI-BLAST Restart
632
\fB\-R\fP (megablast)
633
Report the log information at the end of output
635
\fB\-S\fP\ \fIN\fP (bl2seq, blast2, blastall, blastcl3, megablast)
636
Query strands to search against database for blastn, blastx, tblastx:
648
\fB\-S\fP\ \fIN\fP (blastpgp)
649
Start of required region in query (default = 1)
651
\fB\-S\fP\ \fIN\fP (seedtop)
652
Cutoff cost (default = 30)
654
\fB\-T\fP (bl2seq, blastall, blastcl3, blastpgp, megablast, rpsblast)
657
\fB\-T\fP\ \fIN\fP (blast2)
658
Type of a discontiguous word template:
670
\fB\-U\fP (bl2seq, blastall, blastcl3, blastpgp, megablast, rpsblast)
671
Use lower case filtering for the query sequence
673
\fB\-V\ F\fP (bl2seq, megablast)
674
Allow use of new engine
677
Use variable word size approach to database scanning
679
\fB\-W\fP\ \fIN\fP (bl2seq, blast2, blastall, blastcl3, blastpgp, megablast, rpsblast)
680
Use words of size \fIN\fP (length of best perfect match; zero invokes
681
default behavior, except with megablast, which defaults to 28, and
682
blastpgp, which defaults to 3. The default values for the other
683
commands vary with "program": 11 for blastn, 28 for megablast, and 3
684
for everything else.)
686
\fB\-X\fP\ \fIN\fP (bl2seq, blast2, blastall, blastcl3, blastpgp, megablast, rpsblast, seedtop)
687
X dropoff value for gapped alignment (in bits) (zero invokes default
688
behavior, except with megablast, which defaults to 20, and rpsblast
689
and seedtop, which default to 15. The default values for the other
690
commands vary with "program": 30 for blastn, 20 for megablast, 0 for
691
tblastx, and 15 for everything else.)
693
\fB\-Y\fP\ \fIX\fP (bl2seq, blast2, blastall, blastcl3, blastpgp, rpsblast)
694
Effective length of the search space (use zero for the real size)
696
\fB\-Z\fP\ \fIN\fP (blast2, blastall, blastcl3, blastpgp, megablast, rpsblast)
697
X dropoff value for final [dynamic programming?] gapped alignment in
698
bits (default is 50 for blastn and megablast, 0 for tblastx, 25 for
701
\fB\-a\fP\ \fIfilename\fP (bl2seq)
702
Write SeqAnnot output to \fIfilename\fP
704
\fB\-a\fP\ \fIN\fP (blast2, blastall, blastcl3, blastpgp, impala, megablast, rpsblast)
705
Number of threads to use (default is one)
707
\fB\-b\fP\ \fIN\fP (blast2, blastall, blastcl3, blastpgp, impala, megablast, rpsblast, seedtop)
708
Number of database sequences to show alignments for (B) (default is 250)
713
\fB\-c\fP\ \fIN\fP (blastpgp, impala)
714
Constant in pseudocounts for multipass version (default is 9)
716
\fB\-d\fP\ \fIN\fP (bl2seq)
717
Use theoretical DB size of \fIN\fP (zero stands for the real size)
719
\fB\-d\fP\ \fIstr\fP (blast2, blastall, blastcl3, blastpgp, impala, megablast, seedtop)
720
Database to use (default is nr for all executables except blast2,
721
which requires a second FASTA sequence if this is not set)
723
\fB\-d\fP\ \fIfilename\fP (rpsblast)
727
Expectation value (E) (default = 1e6 for megablast, 10.0 for
730
\fB\-f\fP\ \fIN\fP (blastall, blastcl3)
731
Threshold for extending hits, default if zero: 0 for blastn and
732
megablast, 11 for blastp, 12 for blastx, and 13 for tblasn and
735
\fB\-f\fP\ \fIN\fP (blastpgp)
736
Threshold for extending hits (default 11)
738
\fB\-f\fP (megablast)
739
Show full IDs in the output (default - only GIs or accessions)
741
\fB\-g\ F\fP (bl2seq, blastall, blastcl3, blastpgp, rpsblast)
742
Do not perform gapped alignment (N/A for tblastx)
744
\fB\-g\fP\ \fIN\fP (blast2)
745
Use greedy algorithm for gapped extensions:
755
two-step with ungapped
759
\fB\-g\fP (megablast)
760
Generate words for every base of the database (default is every 4th)
762
\fB\-h\fP\ \fIN\fP (blast2)
763
Frame shift penalty for out-of-frame gapping (blastx, tblastn only;
766
\fB\-h\fP\ \fIX\fP (blastpgp, impala)
767
e-value threshold for inclusion in multipass model (default = 0.002
768
for blastpgp, 0.005 for impala)
770
\fB\-i\fP\ \fIfilename\fP
771
Read (first, query) sequence or set from \fIfilename\fP (default is stdin)
773
\fB\-j\fP\ \fIfilename\fP (bl2seq, blast2)
774
Read second (subject) sequence or set from \fIfilename\fP
776
\fB\-j\fP\ \fIN\fP (blastpgp)
777
Maximum number of passes to use in multipass version (default = 1)
779
\fB\-k\fP\ \fIstr\fP (blast2)
780
Pattern for PHI-BLAST
782
\fB\-k\fP\ \fIfilename\fP (blastpgp, seedtop)
783
Input hit file for PHI-BLAST (default = hit_file)
785
\fB\-l\fP\ \fIstr\fP (blastall, blastpgp, megablast)
786
Restrict search of database to list of GI's [String]
788
\fB\-l\fP\ \fIfilename\fP (rpsblast)
789
Logfile name (default is rpsblast.log)
792
Use Mega Blast for search
794
\fB\-m\fP\ \fIN\fP (blast2, blastall, blastcl3, blastpgp, impala, megablast, rpsblast)
795
alignment view options:
801
query-anchored showing identities
803
query-anchored, no identities
805
flat query-anchored, show identities
807
flat query-anchored, no identities
809
query-anchored, no identities and blunt ends
811
flat query-anchored, no identities and blunt ends
813
XML Blast output (not available for impala)
815
tabular (not available for impala)
817
tabular with comment lines (not available for impala)
819
ASN.1 text (not available for impala or rpsblast)
821
ASN.1 binary (not available for impala or rpsblast)
826
Show GIs in sequence IDs
828
\fB\-n\fP (blastall, blastcl3)
831
\fB\-n\fP (megablast)
832
Use non-greedy (dynamic programming) extension for affine gap scores
834
\fB\-o\fP\ \fIfilename\fP
835
Write final alignment report to \fIfilename\fP rather than stdout
837
\fB\-p\fP\ \fIstr\fP (bl2seq, blast2, blastall, blastcl3)
838
Use the "program" (comparison type) \fIstr\fP. The \fBDESCRIPTION\fP
839
section covers this option in more detail.
841
\fB\-p\fP\ \fIstr\fP (blastpgp)
842
program option for PHI-BLAST (default = blastpgp)
844
\fB\-p\fP\ \fIX\fP (megablast)
845
Identity percentage cut-off (default = 0)
847
\fB\-p\ F\fP (rpsblast)
848
Query sequence is nucleotide, not protein
850
\fB\-p\fP\ \fIstr\fP (seedtop)
855
indicates which patterns occur in a sequence
857
indicates which sequences contain a pattern
861
\fB\-q\fP\ \fIN\fP (bl2seq, blast2, blastall, blastcl3, megablast, seedtop)
862
Penalty for a nucleotide mismatch (blastn only) (default = -10 for
863
seedtop, -3 for everything else)
865
\fB\-q\fP\ \fIN\fP (blastpgp)
866
ASN.1 Scoremat input of checkpoint data:
870
no scoremat input (default)
872
restart from ASCII scoremat checkpoint file
874
restart from binary scoremat checkpoint file
878
\fB\-r\fP\ \fIN\fP (bl2seq, blast2, blastall, blastcl3, megablast, seedtop)
879
Reward for a nucleotide match (blastn only) (default = 10 for seedtop,
880
-10 for everything else)
882
\fB\-s\fP\ \fIN\fP (blast2)
883
Database scanning stride (0 for default behavior)
886
Compute locally optimal Smith-Waterman alignments
888
\fB\-s\fP\ \fIN\fP (megablast)
889
Minimal hit score to report (0 for default behavior)
891
\fB\-t\fP\ \fIN\fP (bl2seq, blast2, blastall, blastcl3)
892
Length of a discontiguous word template (the largest intron allowed in
893
a translated nucleotide sequence when linking multiple distinct
894
assignments; default = 0; negative values disable linking for blastall
897
\fB\-t\ F\fP (blastpgp)
898
Do not use composition-based statistics
900
\fB\-t\fP\ \fIN\fP (megablast)
901
Length of a discontiguous word template (contiguous word if 0 [default])
904
Do only ungapped alignment (always TRUE for tblastx)
906
\fB\-u\fP\ \fIstr\fP (blastcl3)
907
Restrict search of database to results of Entrez2 lookup
909
\fB\-u\fP\ \fIN\fP (blastpgp)
910
ASN.1 Scoremat output of checkpoint data:
914
no scoremat output (default)
916
output ASCII scoremat checkpoint file (requires \fB-J\fP)
918
output binary scoremat checkpoint file (requires \fB-J\fP)
922
\fB\-v\fP\ \fIN\fP (blast2, blastall, blastcl3, blastpgp, impala, megablast,
924
Number of one-line descriptions to show (V) (default = 500)
926
\fB\-w\fP\ \fIN\fP (blast2)
927
Window size (max. allowed distance between a pair of initial hits; 0
928
invokes default behavior)
930
\fB\-w\fP\ \fIN\fP (blastall, blastcl3)
931
Frame shift penalty (OOF algorithm for blastx)
933
\fB\-y\fP\ \fIX\fP (blast2, blastall, blastcl3, blastpgp, impala, rpsblast)
934
X dropoff for ungapped extensions in bits (0.0 invokes default
935
behavior: 20 for blastn, 10 for megablast, and 7 for all others.)
937
\fB\-y\fP\ \fIN\fP (megablast)
938
X dropoff value for ungapped extension (default is 10)
940
\fB\-z\fP\ \fIN\fP (blast2)
941
Longest intron length for uneven gap HSP linking (tblastn only;
944
\fB\-z\fP\ \fIN\fP (blastall, blastcl3, blastpgp, impala, megablast, rpsblast)
945
Effective length of the database (use zero for the real size)
947
This manual page is long and confusing; individual pages might be better.
949
The National Center for Biotechnology Information.
959
<http://www.ncbi.nlm.nih.gov/BLAST/>
added
removed
doc/man/blast.1
