fastf3, fastf3_t - compare a mixed peptide sequence against a
protein database using a modified fasta algorithm.
tfastf3, tfastf3_t - compare a mixed pepide sequence against a
translated DNA database.
fastf3 and tfastf3 are designed to compare a
sequence of mixed peptides to a protein (fastf3) or translated DNA (tfastf3)
database. Unlike the traditional fasta3 search, which uses a protein
or DNA sequence, fastf3 and tfastf3 work with a query sequence
of the form:
>testf from mgstm1
MGCEN,
MIDYP,
MLLAY,
MLLGY
This sequence indicates that a mixture of four peptides has been
found, with 'M' in the first position of each one (as from a CNBr cleavage),
in the second position 'G', 'I', or 'L' (twice), at the third position 'C',
'D', or 'L' (twice), at the fourth position 'E', (included with the
distribution), the mixture is deconvolved to form:
testf MILGY-----------MLLEY-----------MGDAP-----------
::::: ::::: :::::
GT8.7 MPMILGYWNVRGLTHPIRMLLEYTDSSYDEKRYTMGDAPDFDRSQWLNEK
10 20 30 40 50
testf --------------------------------------------------
GT8.7 FKLGLDFPNLPYLIDGSHKITQSNAILRYLARKHHLDGETEEERIRADIV
60 70 80 90 100
20
testf ------------MLCYN
:::::
GT8.7 ENQVMDTRMQLIMLCYNPDFEKQKPEFLKTIPEKMKLYSEFLGKRPWFAG
110 120 130 140 150
fastf3 and tfastf3 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.
- -b #
- number of best scores to show (must be < -E cutoff)
- -d #
- number of best alignments to show ( must be < -E cutoff)
- -D
- turn on debugging mode. Enables checks on sequence alphabet that cause
problems with tfastx3, tfasty3, tfasta3.
- -E #
- Expectation value limit for displaying scores and alignments. Expectation
values for fastf3 and tfastf3 are not as accurate as those
for the other fasta3 programs.
- -H
- turn off histogram display
- -i
- compare against only the reverse complement of the library sequence.
- -L
- report long sequence description in alignments
- -m 0,1,2,3,4,5,6,10
- alignment display options
- -n
- force query to nucleotide sequence
- -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.
- -O file
- send output to file
- -q/-Q
- quiet option; do not prompt for input
- -R file
- save all scores to statistics file
- -S #
- offset substitution matrix values by a constant #
- -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.
- -T #
- (threaded, parallel only) number of threads or workers to use (set by
default to 4 at compile time).
- -t #
- Translation table - tfastf3 can use the BLAST tranlation tables. See
http://www.ncbi.nih.gov/htbin-post/Taxonomy/wprintgc?mode=c/.
- -w #
- line width for similarity score, sequence alignment, output.
- -x "#,#"
- offsets query, library sequence for numbering alignments
- -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.
- -Z db_size
- Set the apparent database size used for expectation value
calculations.
- -1
- Sort by "init1" score.
- -3
- (TFASTF3 only) use only forward frame translations
- FASTLIBS
- location of library choice file (-l FASTLIBS)
- SMATRIX
- default scoring matrix (-s SMATRIX)
- SRCH_URL
- the format string used to define the option to re-search the
database.
- REF_URL
- the format string used to define the option to lookup the library sequence
in entrez, or some other database.
Bill Pearson
wrp@virginia.EDU