.TH FASTF/TFASTFv3 1 local
.SH 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.

.SH DESCRIPTION

.B fastf3
and
.B tfastf3
are designed to compare a sequence of mixed peptides to a protein
(fastf3) or translated DNA (tfastf3) database.  Unlike the traditional
.B fasta3
search, which uses a protein or DNA sequence,
.B fastf3
and
.B tfastf3
work with a query sequence of the form:
.in +5
.nf
>testf from mgstm1
MGCEN,
MIDYP,
MLLAY,
MLLGY
.fi
.in 0
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',
'Y', 'A', or 'G', etc.  When this sequence is compared against mgstm1.aa 
(included with the distribution), the mixture is deconvolved to form:
.nf
.ft C
.in +5
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
.in 0
.ft P
.fi
.SH Options
.LP
.B fastf3
and
.B 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.
.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 fastf3
and
.B tfastf3
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 0,1,2,3,4,5,6,10
alignment display options
.TP
\-n
force query to nucleotide sequence
.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 - tfastf3 can use the BLAST tranlation tables.  See
\fChttp://www.ncbi.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
\-1
Sort by "init1" score.
.TP
\-3
(TFASTF3 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
