Provided by: fasta3_36.3.8h.2020-02-11-4_amd64 bug

NAME

       fasts3,  fasts3_t  -  compare  several  short peptide sequences against a protein database
       using a modified fasta algorithm.

       tfasts3, tfasts3_t - compare short pepides against a translated DNA database.

DESCRIPTION

       fasts3 and tfasts3 are designed to compare set of (presumably non-contiguous) peptides  to
       a  protein  (fasts3)  or  translated  DNA (tfasts3) database.  fasts3/tfasts3 are designed
       particularly for short peptide data from mass-spec analysis of  protein  digests.   Unlike
       the  traditional  fasta3  search, which uses a protein or DNA sequence, fasts3 and tfasts3
       work with a query sequence of the form:
            >tests from mgstm1
            MLLE,
            MILGYW,
            MGADP,
            MLCYNP
     testf    MILGYW----------MLLE------------MGDAP-----------
              ::::::          ::::            :::::
     GT8.7  MPMILGYWNVRGLTHPIRMLLEYTDSSYDEKRYTMGDAPDFDRSQWLNEK
                    10        20        30        40        50

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

     GT8.7  FKLGLDFPNLPYLIDGSHKITQSNAILRYLARKHHLDGETEEERIRADIV
                    60        70        80        90       100

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

Options

       fasts3  and  tfasts3  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 fasts3 and tfasts3 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 0,1,2,3,4,5,6,9,10
              alignment display options

       -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  -  tfasts3  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.

       -3     (TFASTS3 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                             FASTS/TFASTSv3(1)