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PFSEARCH(1) | User Commands | PFSEARCH(1) |
NAME¶
pfsearch - search protein and DNA generalized profiles (legacy)SYNOPSIS¶
pfsearch [ -abCdfhlLmMkrsuvWxyz ] [ profile-file | - ] [ seq-library-file | - ] [ parameters ]DESCRIPTION¶
Build protein and DNA generalized profiles and use them to scan and align sequences, and search databases.OPTIONS¶
-a: report optimal alignment for all sequences.
-b: search complementary strand of DNA sequences.
-f: input sequence file is in FASTA format.
-h: print usage help text.
-l: indicate highest cut-off level (number).
-L: indicate highest cut-off level (text).
-m: report individual matches for circular profiles.
-r: use raw score.
-u: force profile disjointness to UNIQUE.
-C<value>:
- cut-off value. An integer value forces -r. Same as parameter C.
-M<value>:
- set the normalization mode to use for the score computation. Overrides the profile PRIORITY parameter.
- output modifiers:
-d: impose length limit on sequence description.
-k: output using the xPSA header (using keyword=value pairs).
-s: list sequences of the matched regions.
-v: suppress warnings on stderr.
-x: list alignments in PSA format.
-y: list alignments in human readable form.
-z: indicate profile start and stop positions.
-W<value>:
- specifies the output width. Same as parameter W.
- valid (but deprecated) parameters are:
- [C=cut-off-value]
- use option -C instead
- [W=output-width]
- use option -W instead
AUTHOR¶
This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.March 2017 | pfsearch 3 |