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
     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)