fasta35.1

序列对齐 Compare a protein sequence to a protein sequence database or a DNA sequence to a DNA sequenc

.TH FASTA/SSEARCH/FASTX/TFASTXv3 1 local
.SH NAME
fasta35, fasta35_t \- scan a protein or DNA sequence library for similar
sequences

fastx35, fastx35_t \ - compare a DNA sequence to a protein sequence
database, comparing the translated DNA sequence in forward and
reverse frames.

tfastx35, tfastx35_t \ - compare a protein sequence to a DNA sequence
database, calculating similarities with frameshifts to the forward and
reverse orientations.

fasty35, fasty35_t \ - compare a DNA sequence to a protein sequence
database, comparing the translated DNA sequence in forward and reverse
frames.

tfasty35, tfasty35_t \ - compare a protein sequence to a DNA sequence
database, calculating similarities with frameshifts to the forward and
reverse orientations.

fasts35, fasts35_t \- compare unordered peptides to a protein sequence database

fastm35, fastm35_t \- compare ordered peptides (or short DNA sequences)
to a protein (DNA) sequence database

tfasts35, tfasts35_t \- compare unordered peptides to a translated DNA
sequence database

fastf35, fastf35_t \- compare mixed peptides to a protein sequence database

tfastf35, tfastf35_t \- compare mixed peptides to a translated DNA
sequence database

ssearch35, ssearch35_t \- compare a protein or DNA sequence to a
sequence database using the Smith-Waterman algorithm.

ggsearch35, ggsearch35_t \- compare a protein or DNA sequence to a
sequence database using a global alignment (Needleman-Wunsch)

glsearch35, glearch35_t \- compare a protein or DNA sequence to a
sequence database with alignments that are global in the query and
local in the database sequence (global-local).

lalign35 \- produce multiple non-overlapping alignments for protein
and DNA sequences using the Huang and Miller sim algorithm for the
Waterman-Eggert algorithm.

prss35, prfx35 \- (discontinued, replaced by ssearch35 and fastx35)
estimate statistical significance of an alignment by comparing the
score to the distribution of similarity scores generated by shuffling
the second sequence.  prss35 uses Smith-Waterman.  prfx35 uses the
fastx algorithm.

.SH DESCRIPTION

Release 3.4 of the FASTA package provides a modular set of sequence
comparison programs that can run on conventional single processor
computers or in parallel on multiprocessor computers. More than a
dozen programs \- fasta35, fastx35/tfastx35, fasty35/tfasty35,
fasts35/tfasts35, fastm35, fastf35/tfastf35, ssearch35, ggsearch35,
and glsearch35 \- are currently available.

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

Threaded versions of the FASTA programs (fasta35_t, ssearch35_t, etc.)
will run in parallel on modern Linux and Unix multi-core or
multi-processor computers.  Accelerated versions of the Smith-Waterman
algorithm are available for architectures with the Intel SSE2 or
Altivec PowerPC architectures, which can speed-up Smith-Waterman
calculations 10 - 20-fold.

.SH Options for comparison functions
.LP
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 fasta35 and its relatives as part of a WWW page. To
indicate 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:
.sp
.ti 0.5i
cat query.aa | fasta35 -q @:50-150 s
.sp
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.
.TP
\-1
Sort by "init1" score.
.TP
\-3
(TFASTA3, TFASTX/Y35 only) use only forward frame translations
.TP
\-a #
"SHOWALL" option attempts to align all of both sequences in FASTA and SSEARCH.
.TP
\-A
force Smith-Waterman alignment for output.  Smith-Waterman is the
default for protein sequences and FASTX35, but not for TFASTA35 or DNA
comparisons with FASTA35.
.TP
\-b #
number of best scores to show (must be < -E cutoff if -E is given)
.TP
\-B
show z-scores rather than bit scores
.TP
\-c #
threshold for band optimization (FASTA, FASTX)
.TP
\-C #
(fasta35t11d4) length of name abbreviation in alignments, default = 6.
.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 tfastx35, tfasty35, tfasta35.
.TP
\-E #
expectation value upper limit for score and alignment display.
Defaults are 10.0 for FASTA35 and SSEARCH35 protein searches, 5.0 for
translated DNA/protein comparisons, and 2.0 for DNA/DNA searches.
.TP
\-f #
penalty for opening a gap (or first residue for older versions)
.TP
\-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.
.TP
\-g #
penalty for additional residues in a gap
.TP
\-h #
(FASTX35, TFASTX35, FASTY35, TFASTY35 only) penalty for a frameshift between
two codons.
.TP
\-j #
(FASTY35, TFASTY35 only) penalty for a frameshift within a codon.
.TP
\-H
turn off histogram display
.TP
\-i
(DNA only) reverse complement the query sequence. (TFASTX) compare against
only the reverse complement of the library sequence.
.TP
\-k
specify number of shuffles for statistical parameter estimation (default=500).
.TP
\-l str
specify FASTLIBS file
.TP
\-L
report long sequence description in alignments
.TP
\-m 0,1,2,3,4,5,6,9,10,11 alignment display options.  \fC-m 0, 1, 2, 3\fP
display different types of alignments.  \fC-m 4\fP provides an
alignment "map" on the query. \fC-m 5\fP combines the alignment map
and a \fC-m 0\fP alignment.  \fC-m 6\fP provides an HTML output.
\fC-m 9\fP does not change the alignment output, but provides
alignment coordinate and percent identity information with the best
scores report.  \fC-m 9c\fP adds encoded alignment information to the
\fC-m 9\fP; \fC-m 9i\fP provides only percent identity and alignment
length information with the best scores.  With current versions of the
FASTA programs, independent \fC-m\fP options can be combined;
e.g. \fC-m 1 -m 9c -m 6\fP.
.TP
\-m 11 provides \fClav\fP format output from lalign35.  It does not
currently affect other alignment algorithms.  The \fCps_lav\fP
program can be used to convert \fClav\fP format output to postscript
alignment "dot-plots".
.TP
\-M #-#
molecular weight (residue) cutoffs.  -M "101-200" examines only sequences that are 101-200 residues long.
.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
(FASTA) turn fasta band optimization off during initial phase.  This was
the behavior of fasta1.x versions.
.TP
\-O file
send output to file.
.TP
\-q/-Q
quiet option; do not prompt for input
.TP
\-r "+n/-m" 
values for match/mismatch for DNA comparisons. \fC+n\fP is
used for the maximum positive value and \fC-m\fP is used for the
maximum negative value. Values between max and min, are rescaled, but
residue pairs having the value -1 continue to be -1.
.TP 
\-R file
save all scores to statistics file (previously -r file)
.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 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 matrices use 1/3 bit units.  DNA scoring matrices can also
be specified with the "-r" option.
.TP
\-S
treat lower case letters in the query or database as low complexity
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:
.IP
\fCpseg database.fasta -z 1 -q  > database.lc_seg\fP
.TP
\-t #
Translation table - tfasta35, fastx35, tfastx35, fasty35, and
tfasty35 support the BLAST tranlation tables.  See
\fChttp://www.ncbi.nlm.nih.gov/htbin-post/Taxonomy/wprintgc?mode=c/\fP.
.TP
\-T #
(threaded, parallel only) number of threads or workers to use (set by
default to 4 at compile time).
.TP
\-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.
.TP
\-V "?$%*"
Allow special annotation characters in query sequence.  These characters
will be displayed in the alignments on the coordinate number line.
.TP
\-w # line width for similarity score, sequence alignment, output.
.TP
\-W # context length (default is 1/2 of line width -w) for alignment,
like fasta and ssearch, that provide additional sequence context.
.TP
\-x #match,#mismatch
scores used for matches to 'X:X','N:N', '*:*' matches, and the corresponding
'X:not-X', etc, mismatches, overriding the values
specified in the scoring matrix.  If only one value is given, it is
used for both values.
.TP
\-X "#,#"
offsets query, library sequence for numbering alignments
.TP
\-y #
Width for band optimization; by default 16 for DNA and protein ktup=2;
32 for protein ktup=1;
.TP
\-z # Specify statistical calculation. Default is -z 1 for local
similarity searches, which uses regression against the length of the
library sequence. -z -1 disables statistics.  -z 0 estimates
significance without normalizing for sequence length. -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.
.TP
\-Z db_size
Set the apparent database size used for expectation value calculations
(used for protein/protein FASTA and SSEARCH, and for FASTX, FASTY, TFASTX,
and TFASTY).
.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
[e-mail]