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.TH RPSBLAST 1 2001-09-30 NCBI "NCBI Tools User's Manual"
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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-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-S\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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This manual page documents briefly the \fBrpsblast\fP command.
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This manual page was written for the Debian GNU/Linux distribution
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because the original program does not have a manual page.
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A summary of options is included below.
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Cost to extend a gap [Integer]
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Filter query sequence with SEG [String]
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Cost to open a gap [Integer]
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End of required region in query (-1 indicates end of query) [Integer]
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Believe the query defline
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Number of bits to trigger gapping [Real]
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\fB-O\fP\ \fIfilename\fP
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SeqAlign file ('Believe the query defline' must be TRUE) [File Out]
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0 for multiple hits 1-pass, 1 for single hit 1-pass, 2 for 2-pass [Integer]
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Start of required region in query [Integer]
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Use lower case filtering of FASTA sequence
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X dropoff value for gapped alignment (in bits) [Integer]
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Effective length of the search space (use zero for the real size) [Real]
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X dropoff value for final gapped alignment (in bits) [Integer]
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Number of processors to use [Integer]
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Number of database sequence to show alignments for (B) [Integer]
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\fB-d\fP\ \fIfilename\fP
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RPS BLAST Database [File In]
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Expectation value (E) [Real]
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\fB-i\fP\ \fIfilename\fP
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Input query sequence (this parameter must be set) [File In]
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\fB-l\fP\ \fIfilename\fP
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Logfile name [File Out]
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default = rpsblast.log
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alignment view options:
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1 = query-anchored showing identities,
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2 = query-anchored no identities,
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3 = flat query-anchored, show identities,
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4 = flat query-anchored, no identities,
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5 = query-anchored no identities and blunt ends,
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6 = flat query-anchored, no identities and blunt ends,
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7 = XML Blast output,
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8 = tabular output [Integer]
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\fB-o\fP\ \fIfilename\fP
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Output File for Alignment [File Out]
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NOT Query sequence is protein
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Number of database sequences to show one-line descriptions for (V) [Integer]
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Dropoff (X) for blast extensions in bits (default if zero) [Real]
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Effective length of the database (use zero for the real size) [Integer]
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This manual page was written by Aaron M. Ucko <ucko@debian.org>,
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for the Debian GNU/Linux system (but may be used by others).
added
removed
debian/old-blast-man/rpsblast.1
