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

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

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

     fastx3 - compare a  DNA  sequence  to  a  protein
     sequence  database, comparing the translated DNA sequence in
     three frames.

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


DESCRIPTION
     Release 3.0 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.  Four different functions - fasta, tfasta, fastx,
     and tfastx - are currently available.

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


Options for all comparison functions
     -b #  number of best scores to show

     -d #  number of best alignments to show

     -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 0,1,2,3,4,10
          alignment display options

     -n    force query to nucleotide sequence

     -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.   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).

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

     -x "#,#"
          offsets query, library sequence  for  numbering  align-
          ments

Options for FASTA,TFASTA,FASTX
     -1    Sort by "init1" score.

     -3    (TFASTA3, TFASTX3 only) use only forward frame  trans-
          lations

     -A    force Smith-Waterman  alignment  for  output.   Smith-
          Waterman  is  the  default  for  protein  sequences and
          FASTX, but not  for  TFASTA  or  DNA  comparisons  with
          FASTA.

     -c #  threshold for band optimization

     -E #  Expectation value  limit  for  displaying  scores  and
          alignments.  (Typically  10.0 for protein sequence com-
          parisons; 5.0 for FASTX, and 2.0 for DNA sequence  com-
          parisons.)

     -f #  penalty for the first residue in a gap

     -g #  penalty for additional residues in a gap

     -h #  (FASTX, TFASTX only) penalty for a frameshift

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

AUTHOR
     Bill Pearson
     wrp@virginia.EDU