Provided by: fasta3_36.3.8h-2_amd64 
NAME
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.
DESCRIPTION
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
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
Options
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
Environment variables:
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.
AUTHOR
Bill Pearson
wrp@virginia.EDU
local FASTF/TFASTFv3(1)