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

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

     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.

     Options for all 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
          indicate that stdin is to be used, use "-" or "@" as the query
          sequence file name.  "@" is prefered, because one can then specify a
          subset of the query sequence to be used, e.g:

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          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.

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

          -B   Do not show bit score, show z-score instead.

          -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 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 # 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.

          -H   turn off histogram display

          -i   (DNA only) reverse complement the query sequence. (TFASTX)
               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   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 file
               send output to file

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

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          -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 negative
               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 matrices use 1/3 bit units.  DNA
               scoring matrices can also be specified with the "-r" option.

          -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:

               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/Taxonomy/wprintgc?mode=c/.

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

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

          -W # context width (residues outside the aligned region) for fasta3,
               ssearch3 alignments

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

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

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          -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.

          -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).

     Options for FASTA3,TFASTA3,FASTX3,FASTY3,TFASTX3,TFASTY3
          -1   Sort by "init1" score.

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

          -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.

          -c # threshold for band optimization

          -f # penalty for the first residue in a gap

          -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.

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

     SSEARCH3 command line options
          -f # penalty for first residue in a gap

          -g # penalty for additional residues in a gap

     Environment variables:
          FASTLIBS
               location of library choice file (-l FASTLIBS)

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

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