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FASTA/TFASTA/FASTX/TFASTXv3(1) FASTA/TFASTA/FASTX/TFASTXv3(1)



NAME
fasta3, fasta3_t - scan a protein or DNA sequence library for similar
sequences

tfasta3, tfasta3_t - compare a protein sequence to a DNA sequence
library, translating the DNA sequence library `on-the-fly'.

fastx3, fastx3_t - compare a DNA sequence to a protein sequence
database, comparing the translated DNA sequence in forward and reverse
frames.

tfastx3, tfastx3_t - compare a protein sequence to a DNA sequence
database, calculating similarities with frameshifts to the forward and
reverse orientations.

fasty3, fasty3_t - compare a DNA sequence to a protein sequence
database, comparing the translated DNA sequence in forward and reverse
frames.

tfasty3, tfasty3_t - compare a protein sequence to a DNA sequence
database, calculating similarities with frameshifts to the forward and
reverse orientations.

fasts3, fasts3_t - compare unordered peptides to a protein sequence
database

tfasts3, tfasts3_t - compare unordered peptides to a translated DNA
sequence database

fastf3, fastf3_t - compare mixed peptides to a protein sequence
database

tfastf3, tfastf3_t - compare mixed peptides to a translated DNA
sequence database

ssearch3, ssearch3_t - compare a protein or DNA sequence to a sequence
database using the Smith-Waterman algorithm.

prss3, prfx3 - estimate statistical significance of an alignment by
comparing the score to the distribution of similarity scores generated
by shuffling the second sequence. prss3 uses Smith-Waterman. prfx3
uses the fastx algorithm.


DESCRIPTION
Release 3.x of the FASTA package provides a modular set of sequence
comparison programs that can run on conventional single processor com-
puters or in parallel on multiprocessor computers. Seven different pro-
grams - fasta3, fastx3, fasty3, tfastx3, tfasty3, tfasta3, and ssearch3
- are currently available.

All of the comparison programs share a set of basic command line
options; additional options are available for individual comparison
functions.

The fasta3_t, fastx3_t, fasty3_t, tfasta3_t, tfastx3_t, tfasty3_t and
ssearch3_t programs are threaded versions that will run in parallel on
Digital Equipment, Sun, and SGI multiprocessor computers.


Options for comparison functions
These versions of the fasta programs have been modified to 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 indi-
cate that stdin is to be used, use "@" as the query sequence file name.
"@" can also be used to specify a subset of the query sequence to be
used, e.g:

cat query.aa | fasta3 -q @:50-150 s

would search the 's' database with residues 50-150 of query.aa. FASTA
cannot automatically detect the sequence type (protein vs DNA) when
"stdin" is used, so the '-n' option is required for DNA.

-1 Sort by "init1" score.

-3 (TFASTA3, TFASTX/Y3 only) use only forward frame translations

-a # "SHOWALL" option attempts to align all of both sequences in
FASTA and SSEARCH.

-A force Smith-Waterman alignment for output. Smith-Waterman is
the default for protein sequences and FASTX3, but not for
TFASTA3 or DNA comparisons with FASTA3.

-b # number of best scores to show (must be < -E cutoff if -E is
given)

-B show z-scores rather than bit scores

-c # threshold for band optimization (FASTA, FASTX)

-C # (fasta34t11d4) length of name abbreviation in alignments,
default = 6.

-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 upper limit for score and alignment display.
Defaults are 10.0 for FASTA3 and SSEARCH3 protein searches, 5.0
for translated DNA/protein comparisons, and 2.0 for DNA/DNA
searches.

-f # penalty for opening a gap (or first residue for older versions)

-F # expectation value lower limit for score and alignment display.
-F 1e-6 prevents library sequences with E()-values lower than
1e-6 from being displayed. This allows the use to focus on more
distant relationships.

-g # penalty for additional residues in a gap

-h # (FASTX3, TFASTX3, FASTY3, TFASTY3 only) penalty for a frameshift
between two codons.

-j # (FASTY3, TFASTY3 only) penalty for a frameshift within a codon.

-H turn off histogram display

-i (DNA only) reverse complement the query sequence. (TFASTX) com-
pare against only the reverse complement of the library
sequence.

-l str specify FASTLIBS file

-L report long sequence description in alignments

-m 0,1,2,3,4,5,6,9,10 alignment display options. -m 0, 1, 2, 3
display different types of alignments. -m 4 provides an align-
ment "map" on the query. -m 5 combines the alignment map and a
-m 0 alignment. -m 6 provides an HTML output. -m 9 does not
change the alignment output, but provides alignment coordinate
and percent identity information with the best scores report.
-m 9c adds encoded alignment information to the -m 9; -m 9i pro-
vides only percent identity and alignment length information
with the best scores. With current versions of the FASTA pro-
grams, independent -m options can be combined; e.g. -m 1 -m 9c
-m 6.

-M #-# molecular weight (residue) cutoffs. -M "101-200" examines only
sequences that are 101-200 residues long.

-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 (FASTA) turn fasta band optimization off during initial phase.
This was the behavior of fasta1.x versions.

-O file
send output to file

-q/-Q quiet option; do not prompt for input

-r "+n/-m"
values for match/mismatch for DNA comparisons. +n is used for
the maximum positive value and -m is used for the maximum nega-
tive value. Values between max and min, are rescaled, but
residue pairs having the value -1 continue to be -1.

-R file
save all scores to statistics file (previously -r file)

-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 MDM10,
MDM20, MDM40 (Jones, Taylor, and Thornton, 1992 CABIOS
8:275-282; specified as -s M10, -s M20, -s M40). Alternatively,
BLASTP1.4 format scoring matrix files can be specified. BL80,
BL62, and P120 are scaled in 1/2 bit units; all the other matri-
ces use 1/3 bit units. DNA scoring matrices can also be speci-
fied with the "-r" option.

-S treat lower case letters in the query or database as low com-
plexity regions that are equivalent to 'X' during the initial
database scan, but are treated as normal residues for the final
alignment display. Statistical estimates are based on the 'X'ed
out sequence used during the initial search. Protein databases
(and query sequences) can be generated in the appropriate format
using John Wooton's "pseg" program, available from
ftp://ncbi.nlm.nih.gov/pub/seg/pseg. Once you have compiled the
"pseg" program, use the command:

pseg database.fasta -z 1 -q > database.lc_seg

-t # Translation table - tfasta3, fastx3, tfastx3, fasty3, and
tfasty3 now support the BLAST tranlation tables. See
http://www.ncbi.nlm.nih.gov/htbin-post/Taxon-
omy/wprintgc?mode=c/.

-T # (threaded, parallel only) number of threads or workers to use
(set by default to 4 at compile time).

-U Do RNA sequence comparisons: treat 'T' as 'U', allow G:U base
pairs (by scoring "G-A" and "T-C" as "G-G" -1). Search only one
strand.

-V "?$%*"
Allow special annotation characters in query sequence. These
characters will be displayed in the alignments on the coordinate
number line.

-w # line width for similarity score, sequence alignment, output.

-W # context length (default is 1/2 of line width -w) for alignment,
like fasta and ssearch, that provide additional sequence con-
text.

-x # score used for matches to 'X' or 'N', overriding the value spec-
ified in the scoring matrix.

-X "#,#"
offsets query, library sequence for numbering alignments

-y # Width for band optimization; by default 16 for DNA and protein
ktup=2; 32 for protein ktup=1;

-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 provides maximum likelihood estimates
for lambda and K, censoring the 250 lowest and 250 highest
scores. -z 3 uses Altschul and Gish's statistical estimates for
specific protein BLOSUM scoring matrices and gap penalties. -z
4,5: an alternate regression method. -z 6 uses a composition
based maximum likelihood estimate based on the method of Mott
(1992) Bull. Math. Biol. 54:59-75. -z 11,12,14,15,16: compute
the regression against scores of randomly shuffled copies of the
library sequences. Twice as many comparisons are performed, but
accurate estimates can be generated from databases of related
sequences. -z 11 uses the -z 1 regression strategy, etc.

-Z db_size
Set the apparent database size used for expectation value calcu-
lations (used for protein/protein FASTA and SSEARCH, and for
FASTX, FASTY, TFASTX, and TFASTY).

Environmental 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