NAME

       fastf3,  fastf3_t  -  compare  a mixed peptide sequence against a protein database using a modified fasta
       algorithm.

       tfastf3, tfastf3_t - compare a mixed pepide sequence against a translated DNA database.

DESCRIPTION

       fastf3 and tfastf3 are designed to compare a  sequence  of  mixed  peptides  to  a  protein  (fastf3)  or
       translated  DNA  (tfastf3)  database.   Unlike the traditional fasta3 search, which uses a protein or DNA
       sequence, fastf3 and tfastf3 work with a query sequence of the form:
            >testf from mgstm1
            MGCEN,
            MIDYP,
            MLLAY,
            MLLGY
form:
     testf    MILGY-----------MLLEY-----------MGDAP-----------
              :::::           :::::           :::::
     GT8.7  MPMILGYWNVRGLTHPIRMLLEYTDSSYDEKRYTMGDAPDFDRSQWLNEK
                    10        20        30        40        50

     testf  --------------------------------------------------

     GT8.7  FKLGLDFPNLPYLIDGSHKITQSNAILRYLARKHHLDGETEEERIRADIV
                    60        70        80        90       100

                           20
     testf  ------------MLCYN
                        :::::
     GT8.7  ENQVMDTRMQLIMLCYNPDFEKQKPEFLKTIPEKMKLYSEFLGKRPWFAG
                   110       120       130       140       150

Options

       fastf3  and  tfastf3  can  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.

       -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 limit for displaying scores and alignments.  Expectation values for  fastf3  and
              tfastf3 are not as accurate as those for the other fasta3 programs.

       -H     turn off histogram display

       -i     compare against only the reverse complement of the library sequence.

       -L     report long sequence description in alignments

       -m 0,1,2,3,4,5,6,10
              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

       -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.  With this version, many more scoring matrices are
              available, including BLOSUM80 (BL80), and MDM_10, MDM_20, MDM_40 (M10, M20,  M40).  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).

       -t #   Translation   table    -    tfastf3    can    use    the    BLAST    tranlation    tables.     See
              http://www.ncbi.nih.gov/htbin-post/Taxonomy/wprintgc?mode=c/.

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

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

       -z #   Specify  statistical calculation. Default is -z 1, which uses regression against the length of the
              library sequence. -z 0 disables statistics.  -z 2 uses the  ln()  length  correction.  -z  3  uses
              Altschul  and  Gish's  statistical  estimates for specific protein BLOSUM scoring matrices and gap
              penalties. -z 4: an alternate regression method.

       -Z db_size
              Set the apparent database size used for expectation value calculations.

       -1     Sort by "init1" score.

       -3     (TFASTF3 only) use only forward frame translations

Environment 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

                                                      local                                    FASTF/TFASTFv3(1)