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+.TH FASTA/TFASTA/FASTX/TFASTXv3 1 local
+.SH 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.
+
+.SH DESCRIPTION
+
+Release 3.x 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. Seven different
+programs \- 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.
+
+.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 fasta3 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 | fasta3 -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/Y3 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 FASTX3, but not for TFASTA3 or DNA
+comparisons with FASTA3.
+.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 #
+(fasta34t11d4) 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 tfastx3, tfasty3, tfasta3.
+.TP
+\-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.
+.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 #
+(FASTX3, TFASTX3, FASTY3, TFASTY3 only) penalty for a frameshift between
+two codons.
+.TP
+\-j #
+(FASTY3, TFASTY3 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
+\-l str
+specify FASTLIBS file
+.TP
+\-L
+report long sequence description in alignments
+.TP
+\-m 0,1,2,3,4,5,6,9,10 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 #-#
+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 - tfasta3, fastx3, tfastx3, fasty3, and
+tfasty3 now support the BLAST tranlation tables.  See
+\fChttp://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi\fP.
+.IP
+In addition, "\-t t" or "\-t t#" turns on the addition of an implicit termination
+codon to a protein:translated DNA match.  That is, each protein
+sequence implicitly ends with "*", which matches the termination codes
+for the appropriate genetic code.  "\-t t#" sets implicit termination
+and a different genetic code.
+.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, which uses
+regression against the length of the library sequence. -z 0 disables
+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.
+.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
+wrp@virginia.EDU