+++ /dev/null
-.TH FASTS/TFASTSv3 1 local
-.SH NAME
-fasts3, fasts3_t \- compare several short peptide sequences against a protein
-database using a modified fasta algorithm.
-
-tfasts3, tfasts3_t \- compare short pepides against a
-translated DNA database.
-
-.SH DESCRIPTION
-
-.B fasts3
-and
-.B tfasts3
-are designed to compare set of (presumably non-contiguous) peptides to
-a protein (fasts3) or translated DNA (tfasts3) database.
-fasts3/tfasts3 are designed particularly for short peptide data from
-mass-spec analysis of protein digests. Unlike the traditional
-.B fasta3
-search, which uses a protein or DNA sequence,
-.B fasts3
-and
-.B tfasts3
-work with a query sequence of the form:
-.in +5
-.nf
->tests from mgstm1
-MLLE,
-MILGYW,
-MGADP,
-MLCYNP
-.fi
-.in 0
-This sequence indicates that four peptides are to be used. When this
-sequence is compared against mgstm1.aa (included with the
-distribution), the result is:
-.nf
-.ft C
-.in +5
-testf MILGYW----------MLLE------------MGDAP-----------
- :::::: :::: :::::
-GT8.7 MPMILGYWNVRGLTHPIRMLLEYTDSSYDEKRYTMGDAPDFDRSQWLNEK
- 10 20 30 40 50
-
-testf --------------------------------------------------
-
-GT8.7 FKLGLDFPNLPYLIDGSHKITQSNAILRYLARKHHLDGETEEERIRADIV
- 60 70 80 90 100
-
- 20
-testf ------------MLCYNP
- ::::::
-GT8.7 ENQVMDTRMQLIMLCYNPDFEKQKPEFLKTIPEKMKLYSEFLGKRPWFAG
- 110 120 130 140 150
-.in 0
-.ft P
-.fi
-.SH Options
-.LP
-.B fasts3
-and
-.B tfasts3
-can accept a query sequence from the unix "stdin" data stream. This makes it much
-easier to use fasta3 and its relatives as part of a WWW page. To
-indicate that stdin is to be used, use "-" or "@" as the query
-sequence file name.
-.TP
-\-b #
-number of best scores to show (must be < -E cutoff)
-.TP
-\-d #
-number of best alignments to show ( must be < -E cutoff)
-.TP
-\-D
-turn on debugging mode. Enables checks on sequence alphabet that
-cause problems with tfastx3, tfasty3, tfasta3.
-.TP
-\-E #
-Expectation value limit for displaying scores and
-alignments. Expectation values for
-.B fasts3
-and
-.B tfasts3
-are not as accurate as those for the other
-.B fasta3
-programs.
-.TP
-\-H
-turn off histogram display
-.TP
-\-i
-compare against only the reverse complement of the library sequence.
-.TP
-\-L
-report long sequence description in alignments
-.TP
-\-m 0,1,2,3,4,5,6,9,10
-alignment display options
-.TP
-\-N #
-break long library sequences into blocks of # residues. Useful for
-bacterial genomes, which have only one sequence entry. -N 2000 works
-well for well for bacterial genomes.
-.TP
-\-O file
-send output to file
-.TP
-\-q/-Q
-quiet option; do not prompt for input
-.TP
-\-R file
-save all scores to statistics file
-.TP
-\-S #
-offset substitution matrix values by a constant #
-.TP
-\-s name
-specify substitution matrix. BLOSUM50 is used by default;
-PAM250, PAM120, and BLOSUM62 can be specified by setting -s P120,
-P250, or BL62. With this version, many more scoring matrices are
-available, including BLOSUM80 (BL80), and MDM_10, MDM_20, MDM_40 (M10,
-M20, M40). Alternatively, BLASTP1.4 format scoring matrix files can be
-specified.
-.TP
-\-T #
-(threaded, parallel only) number of threads or workers to use (set by
-default to 4 at compile time).
-.TP
-\-t #
-Translation table - tfasts3 can use the BLAST tranlation tables. See
-\fChttp://www.ncbi.nlm.nih.gov/htbin-post/Taxonomy/wprintgc?mode=c/\fP.
-.TP
-\-w #
-line width for similarity score, sequence alignment, output.
-.TP
-\-x "#,#"
-offsets query, library sequence for numbering alignments
-.TP
-\-z #
-Specify statistical calculation. Default is -z 1, which uses
-regression against the length of the library sequence. -z 0 disables
-statistics. -z 2 uses the ln() length correction. -z 3 uses Altschul
-and Gish's statistical estimates for specific protein BLOSUM scoring
-matrices and gap penalties. -z 4: an alternate regression method.
-.TP
-\-Z db_size
-Set the apparent database size used for expectation value calculations.
-.TP
-\-3
-(TFASTS3 only) use only forward frame translations
-.SH Environment variables:
-.TP
-FASTLIBS
-location of library choice file (-l FASTLIBS)
-.TP
-SMATRIX
-default scoring matrix (-s SMATRIX)
-.TP
-SRCH_URL
-the format string used to define the option to re-search the
-database.
-.TP
-REF_URL
-the format string used to define the option to lookup the library
-sequence in entrez, or some other database.
-
-.SH AUTHOR
-Bill Pearson
-.br
-wrp@virginia.EDU
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