.TH FASTS/TFASTSv3 1 local
.SH NAME
fasts3, fasts3_t \- compare several short peptide sequences against a protein
database using a modified fasta algorithm.

tfasts3, tfasts3_t \- compare short pepides against a
translated DNA database.

.SH DESCRIPTION

.B fasts3
and
.B tfasts3
are designed to compare set of (presumably non-contiguous) peptides to
a protein (fasts3) or translated DNA (tfasts3) database.
fasts3/tfasts3 are designed particularly for short peptide data from
mass-spec analysis of protein digests.  Unlike the traditional
.B fasta3
search, which uses a protein or DNA sequence,
.B fasts3
and
.B tfasts3
work with a query sequence of the form:
.in +5
.nf
>tests from mgstm1
MLLE,
MILGYW,
MGADP,
MLCYNP
.fi
.in 0
This sequence indicates that four peptides are to be used.  When this
sequence is compared against mgstm1.aa (included with the
distribution), the result is:
.nf
.ft C
.in +5
testf    MILGYW----------MLLE------------MGDAP-----------
         ::::::          ::::            :::::           
GT8.7  MPMILGYWNVRGLTHPIRMLLEYTDSSYDEKRYTMGDAPDFDRSQWLNEK
               10        20        30        40        50

testf  --------------------------------------------------
                                                         
GT8.7  FKLGLDFPNLPYLIDGSHKITQSNAILRYLARKHHLDGETEEERIRADIV
               60        70        80        90       100

                      20                                 
testf  ------------MLCYNP
                   ::::::
GT8.7  ENQVMDTRMQLIMLCYNPDFEKQKPEFLKTIPEKMKLYSEFLGKRPWFAG
              110       120       130       140       150
.in 0
.ft P
.fi
.SH Options
.LP
.B fasts3
and
.B tfasts3
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 fasts3
and
.B tfasts3
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 0,1,2,3,4,5,6,9,10
alignment display options
.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 - tfasts3 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
\-3
(TFASTS3 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
