1 .TH FASTS/TFASTSv3 1 local
3 fasts3, fasts3_t \- compare several short peptide sequences against a protein
4 database using a modified fasta algorithm.
6 tfasts3, tfasts3_t \- compare short pepides against a
7 translated DNA database.
14 are designed to compare set of (presumably non-contiguous) peptides to
15 a protein (fasts3) or translated DNA (tfasts3) database.
16 fasts3/tfasts3 are designed particularly for short peptide data from
17 mass-spec analysis of protein digests. Unlike the traditional
19 search, which uses a protein or DNA sequence,
23 work with a query sequence of the form:
33 This sequence indicates that four peptides are to be used. When this
34 sequence is compared against mgstm1.aa (included with the
35 distribution), the result is:
39 testf MILGYW----------MLLE------------MGDAP-----------
41 GT8.7 MPMILGYWNVRGLTHPIRMLLEYTDSSYDEKRYTMGDAPDFDRSQWLNEK
44 testf --------------------------------------------------
46 GT8.7 FKLGLDFPNLPYLIDGSHKITQSNAILRYLARKHHLDGETEEERIRADIV
50 testf ------------MLCYNP
52 GT8.7 ENQVMDTRMQLIMLCYNPDFEKQKPEFLKTIPEKMKLYSEFLGKRPWFAG
62 can accept a query sequence from the unix "stdin" data stream. This makes it much
63 easier to use fasta3 and its relatives as part of a WWW page. To
64 indicate that stdin is to be used, use "-" or "@" as the query
68 number of best scores to show (must be < -E cutoff)
71 number of best alignments to show ( must be < -E cutoff)
74 turn on debugging mode. Enables checks on sequence alphabet that
75 cause problems with tfastx3, tfasty3, tfasta3.
78 Expectation value limit for displaying scores and
79 alignments. Expectation values for
83 are not as accurate as those for the other
88 turn off histogram display
91 compare against only the reverse complement of the library sequence.
94 report long sequence description in alignments
96 \-m 0,1,2,3,4,5,6,9,10
97 alignment display options
100 break long library sequences into blocks of # residues. Useful for
101 bacterial genomes, which have only one sequence entry. -N 2000 works
102 well for well for bacterial genomes.
108 quiet option; do not prompt for input
111 save all scores to statistics file
114 offset substitution matrix values by a constant #
117 specify substitution matrix. BLOSUM50 is used by default;
118 PAM250, PAM120, and BLOSUM62 can be specified by setting -s P120,
119 P250, or BL62. With this version, many more scoring matrices are
120 available, including BLOSUM80 (BL80), and MDM_10, MDM_20, MDM_40 (M10,
121 M20, M40). Alternatively, BLASTP1.4 format scoring matrix files can be
125 (threaded, parallel only) number of threads or workers to use (set by
126 default to 4 at compile time).
129 Translation table - tfasts3 can use the BLAST tranlation tables. See
130 \fChttp://www.ncbi.nlm.nih.gov/htbin-post/Taxonomy/wprintgc?mode=c/\fP.
133 line width for similarity score, sequence alignment, output.
136 offsets query, library sequence for numbering alignments
139 Specify statistical calculation. Default is -z 1, which uses
140 regression against the length of the library sequence. -z 0 disables
141 statistics. -z 2 uses the ln() length correction. -z 3 uses Altschul
142 and Gish's statistical estimates for specific protein BLOSUM scoring
143 matrices and gap penalties. -z 4: an alternate regression method.
146 Set the apparent database size used for expectation value calculations.
149 (TFASTS3 only) use only forward frame translations
150 .SH Environment variables:
153 location of library choice file (-l FASTLIBS)
156 default scoring matrix (-s SMATRIX)
159 the format string used to define the option to re-search the
163 the format string used to define the option to lookup the library
164 sequence in entrez, or some other database.