1 .TH FASTF/TFASTFv3 1 local
3 fastf3, fastf3_t \- compare a mixed peptide sequence against a protein
4 database using a modified fasta algorithm.
6 tfastf3, tfastf3_t \- compare a mixed pepide sequence against a
7 translated DNA database.
14 are designed to compare a sequence of mixed peptides to a protein
15 (fastf3) or translated DNA (tfastf3) database. Unlike the traditional
17 search, which uses a protein or DNA sequence,
21 work with a query sequence of the form:
31 This sequence indicates that a mixture of four peptides has been
32 found, with 'M' in the first position of each one (as from a CNBr
33 cleavage), in the second position 'G', 'I', or 'L' (twice), at the
34 third position 'C', 'D', or 'L' (twice), at the fourth position 'E',
35 'Y', 'A', or 'G', etc. When this sequence is compared against mgstm1.aa
36 (included with the distribution), the mixture is deconvolved to form:
40 testf MILGY-----------MLLEY-----------MGDAP-----------
42 GT8.7 MPMILGYWNVRGLTHPIRMLLEYTDSSYDEKRYTMGDAPDFDRSQWLNEK
45 testf --------------------------------------------------
47 GT8.7 FKLGLDFPNLPYLIDGSHKITQSNAILRYLARKHHLDGETEEERIRADIV
51 testf ------------MLCYN
53 GT8.7 ENQVMDTRMQLIMLCYNPDFEKQKPEFLKTIPEKMKLYSEFLGKRPWFAG
63 can accept a query sequence from the unix "stdin" data stream. This makes it much
64 easier to use fasta3 and its relatives as part of a WWW page. To
65 indicate that stdin is to be used, use "-" or "@" as the query
69 number of best scores to show (must be < -E cutoff)
72 number of best alignments to show ( must be < -E cutoff)
75 turn on debugging mode. Enables checks on sequence alphabet that
76 cause problems with tfastx3, tfasty3, tfasta3.
79 Expectation value limit for displaying scores and
80 alignments. Expectation values for
84 are not as accurate as those for the other
89 turn off histogram display
92 compare against only the reverse complement of the library sequence.
95 report long sequence description in alignments
98 alignment display options
101 force query to nucleotide sequence
104 break long library sequences into blocks of # residues. Useful for
105 bacterial genomes, which have only one sequence entry. -N 2000 works
106 well for well for bacterial genomes.
112 quiet option; do not prompt for input
115 save all scores to statistics file
118 offset substitution matrix values by a constant #
121 specify substitution matrix. BLOSUM50 is used by default;
122 PAM250, PAM120, and BLOSUM62 can be specified by setting -s P120,
123 P250, or BL62. With this version, many more scoring matrices are
124 available, including BLOSUM80 (BL80), and MDM_10, MDM_20, MDM_40 (M10,
125 M20, M40). Alternatively, BLASTP1.4 format scoring matrix files can be
129 (threaded, parallel only) number of threads or workers to use (set by
130 default to 4 at compile time).
133 Translation table - tfastf3 can use the BLAST tranlation tables. See
134 \fChttp://www.ncbi.nlm.nih.gov/htbin-post/Taxonomy/wprintgc?mode=c/\fP.
137 line width for similarity score, sequence alignment, output.
140 offsets query, library sequence for numbering alignments
143 Specify statistical calculation. Default is -z 1, which uses
144 regression against the length of the library sequence. -z 0 disables
145 statistics. -z 2 uses the ln() length correction. -z 3 uses Altschul
146 and Gish's statistical estimates for specific protein BLOSUM scoring
147 matrices and gap penalties. -z 4: an alternate regression method.
150 Set the apparent database size used for expectation value calculations.
153 Sort by "init1" score.
156 (TFASTF3 only) use only forward frame translations
157 .SH Environment variables:
160 location of library choice file (-l FASTLIBS)
163 default scoring matrix (-s SMATRIX)
166 the format string used to define the option to re-search the
170 the format string used to define the option to lookup the library
171 sequence in entrez, or some other database.