FASTS/TFASTSv3(1) FASTS/TFASTSv3(1)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.
DESCRIPTIONfasts3 and tfasts3 are designed to compare set of (presumably non-con‐
tiguous) 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 tradi‐
tional fasta3 search, which uses a protein or DNA sequence, fasts3 and
tfasts3 work with a query sequence of the form:
>tests from mgstm1
MLLE,
MILGYW,
MGADP,
MLCYNP
This sequence indicates that four peptides are to be used. When this sequenceis compared against mgstm1.aa (included with the distribution), the result is:
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
Optionsfasts3 and 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.
-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 fasts3 and tfasts3 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 0,1,2,3,4,5,6,9,10
alignment display options
-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 - tfasts3 can use the BLAST tranlation tables.
See http://www.ncbi.nih.gov/htbin-post/Taxon‐
omy/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 dis‐
ables statistics. -z 2 uses the ln() length correction. -z 3
uses Altschul and Gish's statistical estimates for specific pro‐
tein BLOSUM scoring matrices and gap penalties. -z 4: an alter‐
nate regression method.
-Z db_size
Set the apparent database size used for expectation value calcu‐
lations.
-3 (TFASTS3 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 FASTS/TFASTSv3(1)
