Provided by: fasta3_36.3.8i.14-Nov-2020-1_amd64 bug

NAME

       fasta36 - scan a protein or DNA sequence library for similar sequences

       fastx36  - compare a DNA sequence to a protein sequence database, comparing the translated
       DNA sequence in forward and reverse frames.

       tfastx36   -  compare  a  protein  sequence  to  a  DNA  sequence  database,   calculating
       similarities with frameshifts to the forward and reverse orientations.

       fasty36  - compare a DNA sequence to a protein sequence database, comparing the translated
       DNA sequence in forward and reverse frames.

       tfasty36   -  compare  a  protein  sequence  to  a  DNA  sequence  database,   calculating
       similarities with frameshifts to the forward and reverse orientations.

       fasts36 - compare unordered peptides to a protein sequence database

       fastm36  -  compare  ordered peptides (or short DNA sequences) to a protein (DNA) sequence
       database

       tfasts36 - compare unordered peptides to a translated DNA sequence database

       fastf36 - compare mixed peptides to a protein sequence database

       tfastf36 - compare mixed peptides to a translated DNA sequence database

       ssearch36 - compare a protein or DNA sequence to a  sequence  database  using  the  Smith-
       Waterman algorithm.

       ggsearch36  -  compare  a  protein  or  DNA sequence to a sequence database using a global
       alignment (Needleman-Wunsch)

       glsearch36 - compare a protein or DNA sequence to a sequence database with alignments that
       are global in the query and local in the database sequence (global-local).

       lalign36 - produce multiple non-overlapping alignments for protein and DNA sequences using
       the Huang and Miller sim algorithm for the Waterman-Eggert algorithm.

       prss36,  prfx36  -  discontinued;  all  the  FASTA  programs  will  estimate   statistical
       significance using 500 shuffled sequence scores if two sequences are compared.

DESCRIPTION

       Release  3.6  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.  More  than  a  dozen  programs  - fasta36, fastx36/tfastx36, fasty36/tfasty36,
       fasts36/tfasts36, fastm36, fastf36/tfastf36, ssearch36, ggsearch36, and glsearch36  -  are
       currently available.

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

       Threaded versions of the FASTA programs (built by default under Unix/Linux/MacOX)  run  in
       parallel  on  modern  Linux and Unix multi-core or multi-processor computers.  Accelerated
       versions of the Smith-Waterman algorithm are available for architectures  with  the  Intel
       SSE2 or Altivec PowerPC architectures, which can speed-up Smith-Waterman calculations 10 -
       20-fold.

       In addition to the serial and threaded  versions  of  the  FASTA  programs,  MPI  parallel
       versions  are  available as fasta36_mpi, ssearch36_mpi, fastx36_mpi, etc. The MPI parallel
       versions use the same command line options as the serial and threaded versions.

Running the FASTA programs

       By default, the FASTA programs are no longer interactive; they are run  from  the  command
       line  by  specifying  the  program,  query.file,  and  library.file.  Program options must
       preceed the query.file and library.file arguments:

     fasta36 -option1 -option2 -option3 query.file library.file > fasta.output

       The "classic" interactive mode, which  prompts  for  a  query.file  and  library.file,  is
       available  with  the  -I  option.  Typing a program name without any arguments (ssearch36)
       provides a short help message; program_name -help  provides  a  complete  set  of  program
       options.

       Program options MUST preceed the query.file and library.file arguments.

FASTA program options

       The  default  scoring  matrix  and  gap  penalties  used by each of the programs have been
       selected for high sensitivity searches with the various algorithms.  The  default  program
       behavior  can  be  modified  by  providing  command line options before the query.file and
       library.file arguments.  Command line options can also be used in interactive mode.

       Command line arguments come in several classes.

       (1) Commands that specify the comparison type. FASTA, FASTS, FASTM, SSEARCH, GGSEARCH, and
       GLSEARCH  can  compare  either  protein  or  DNA  sequences,  and attempt to recognize the
       comparison type by looking the residue composition. -n, -p  specify  DNA  (nucleotide)  or
       protein comparison, respectively. -U specifies RNA comparison.

       (2) Commands that limit the set of sequences compared: -1, -3, -M.

       (3)  Commands  that  modify  the  scoring  parameters: -f gap-open penaltyP, -g gap-extend
       penalty, -j  inter-codon  frame-shift,  within-codon  frameshift,  -s  scoring-matrix,  -r
       match/mismatch score, -x X:X score.

       (4)  Commands that modify the algorithm (mostly FASTA and [T]FASTX/Y): -c, -w, -y, -o. The
       -S can be used to ignore lower-case (low complexity) residues  during  the  initial  score
       calculation.

       (5) Commands that modify the output: -A, -b number, -C width, -d number, -L, -m 0-11,B, -w
       line-width, -W context-width, -o offset1,ofset2

       (6) Commands that affect statistical estimates: -Z, -k.

Option summary:

       -1     Sort by "init1" score (obsolete)

       -3     ([t]fast[x,y] only) use only forward frame translations

       -a     Displays the full length  (included  unaligned  regions)  of  both  sequences  with
              fasta36, ssearch36, glsearch36, and fasts36.

       -A (fasta36 only) For DNA:DNA, force Smith-Waterman alignment for
              output.    Smith-Waterman   is   the   default  for  FASTA  protein  alignment  and
              [t]fast[x,y], but not for DNA comparisons with  FASTA.   For  protein:protein,  use
              band-alignment algorithm.

       -b #   number  of  best scores/descriptions to show (must be < expectation cutoff if -E is
              given).  By default, this option is no longer used;  all  scores  better  than  the
              expectation   (E())   cutoff   are   listed.   To   guarantee   the  display  of  #
              descriptions/scores, use -b =#, i.e. -b =100 ensures that  100  descriptions/scores
              will  be  displayed.   To  guarantee at least 1 description, but possibly many more
              (limited by -E e_cut), use -b >1.

       -c "E-opt E-join"
              threshold for gap joining (E-join) and  band  optimization  (E-opt)  in  FASTA  and
              [T]FASTX/Y.   FASTA36  now  uses  BLAST-like statistical thresholds for joining and
              band optimization.  The default statistical thresholds for protein  and  translated
              comparisons  are  E-opt=0.2, E-join=0.5; for DNA, E-join = 0.1 and E-opt= 0.02. The
              actual number of joins and optimizations is reported after  the  E-join  and  E-opt
              scoring  parameters.   Statistical  thresholds  improves  search  speed 2 - 3X, and
              provides much more accurate statistical estimates for matrices other than BLOSUM50.
              The  "classic" joining/optimization thresholds that were the default in fasta35 and
              earlier programs are available using -c O (upper case O), possibly followed a value
              > 1.0 to set the optcut optimization threshold.

       -C #   length of name abbreviation in alignments, default = 6.  Must be less than 20.

       -d #   number of best alignments to show ( must be < expectation (-E) cutoff and <= the -b
              description limit).

       -D     turn on debugging mode.  Enables checks on sequence alphabet  that  cause  problems
              with tfastx36, tfasty36 (only available after compile time option).  Also preserves
              temp files with -e expand_script.sh option.

       -e expand_script.sh
              Run a script to expand the set of sequences displayed/aligned based on the  results
              of  the  initial  search.   When  the -e expand_script.sh option is used, after the
              initial scan and statistics calculation, but before the "Best  scores"  are  shown,
              expand_script.sh  with  a  single  argument,  the  name of a file that contains the
              accession information (the text on the fasta description line  between  >  and  the
              first  space)  and the E()-value for the sequence.  expand_script.sh then uses this
              information to send a library of additional sequences to stdout.  These  additional
              sequences  are  included in the list of high-scoring sequences (if their scores are
              significant) and aligned. The additional sequences do not change the statistics  or
              database size.

       -E e_cut e_cut_r
              expectation  value  upper limit for score and alignment display.  Defaults are 10.0
              for  FASTA36  and  SSEARCH36  protein  searches,  5.0  for  translated  DNA/protein
              comparisons,  and 2.0 for DNA/DNA searches. FASTA version 36 now reports additional
              alignments between the query and the library sequence, the second  value  sets  the
              threshold   for  the  subsequent  alignments.   If  not  given,  the  threshold  is
              e_cut/10.0.  If given and value > 1.0, e_cut_r = e_cut / value; for  value  <  1.0,
              e_cut_r = value;  If e_cut_r < 0, then the additional alignment option is disabled.

       -f #   penalty for opening a gap.

       -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.

       -g #   penalty for additional residues in a gap

       -h     Show short help message.

       -help  Show long help message, with all options.

       -H     show histogram (with fasta-36.3.4, the histogram is not shown by default).

       -i     (fasta  DNA,  [t]fastx[x,y])  compare  against  only  the reverse complement of the
              library sequence.

       -I     interactive mode; prompt for query filename, library.

       -j # # ([t]fast[x,y] only) penalty for a frameshift between two  codons,  ([t]fasty  only)
              penalty for a frameshift within a codon.

       -J     (lalign36 only) show identity alignment.

       -k     specify number of shuffles for statistical parameter estimation (default=500).

       -l str specify FASTLIBS file

       -L     report long sequence description in alignments (up to 200 characters).

       -m 0,1,2,3,4,5,6,8,9,10,11,B,BB,"F# out.file" alignment display
              options.   -m  0,  1, 2, 3 display different types of alignments.  -m 4 provides an
              alignment "map" on the query. -m 5 combines the alignment map and a -m 0 alignment.
              -m 6 provides an HTML output.

       -m 8 seeks to mimic BLAST -m 8 tabular output.  Only query and
              library  sequence  names, and identity, mismatch, starts/stops, E()-values, and bit
              scores are displayed.  -m 8C mimics BLAST tabular format with comment lines.  -m  8
              formats do not show alignments.

       -m 9 does not change the alignment output, but provides
              alignment  coordinate and percent identity information with the best scores report.
              -m 9c adds encoded alignment information to the -m 9; -m 9C adds encoded  alignment
              information  as  a  CIGAR  formatted  string.  To accomodate frameshifts, the CIGAR
              format has been supplemented with F (forward) and R (reverse).  -m 9i provides only
              percent  identity  and  alignment  length  information  with the best scores.  With
              current versions of the FASTA programs, independent -m  options  can  be  combined;
              e.g. -m 1 -m 9c -m 6.

       -m 11 provides lav format output from lalign36.  It does not
              currently  affect  other alignment algorithms.  The lav2ps and lav2svg programs can
              be used to convert lav format output to postscript/SVG alignment "dot-plots".

       -m B provides BLAST-like alignments.  Alignments are labeled as
              "Query" and "Sbjct", with coordinates on the same line as the sequences, and BLAST-
              like  symbols for matches and mismatches. -m BB extends BLAST similarity to all the
              output, providing an output that closely mimics BLAST output.

       -m "F# out.file" allows one search to write different alignment
              formats to different files.  The 'F' indicates separate file output; the '#' is the
              output  format  (1-6,8,9,10,11,B,BB,  multiple  compatible  formats can be combined
              separated by commas -',').

       -M #-# molecular weight (residue) cutoffs.  -M "101-200" examines only  library  sequences
              that are 101-200 residues long.

       -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. (This option was required when FASTA only provided one alignment
              between the query and library sequence.  It is not as  useful,  now  that  multiple
              alignments are available.)

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

       -O file
              send output to file.

       -p     force query to protein alphabet.

       -P pssm_file
              (ssearch36,  ggsearch36, glsearch36 only).  Provide blastpgp checkpoint file as the
              PSSM for searching. Two PSSM file formats are available,  which  must  be  provided
              with  the  filename.  'pssm_file  0' uses a binary format that is machine specific;
              'pssm_file  1'  uses  the  "blastpgp  -u  1  -C  pssm_file"  ASN.1  binary   format
              (preferred).

       -q/-Q  quiet option; do not prompt for input (on by default)

       -r "+n/-m"
              (DNA  only)  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.  Additional scoring
              matrices include: BLOSUM80 (BL80), and MDM10,  MDM20,  MDM40  (Jones,  Taylor,  and
              Thornton,  1992  CABIOS 8:275-282; specified as -s MD10, -s MD20, -s MD40), OPTIMA5
              (-s OPT5, Kann and Goldstein, (2002) Proteins 48:367-376), and VTML160  (-s  VT160,
              Mueller  and  Vingron  (2002)  J.  Comp.  Biol.  19:8-13).  Each scoring matrix has
              associated default gap penalties.  The  BLOSUM62  scoring  matrix  and  -11/-1  gap
              penalties can be specified with -s BP62.

              Alternatively,  a  BLASTP  format  scoring  matrix  file  can be specified, e.g. -s
              matrix.filename.  DNA scoring matrices can also be specified with the "-r" option.

              With fasta36.3, variable scoring  matrices  can  be  specified  by  preceeding  the
              scoring  matrix  abbreviation  with '?', e.g. -s '?BP62'. Variable scoring matrices
              allow the FASTA programs to  choose  an  alternative  scoring  matrix  with  higher
              information content (bit score/position) when short queries are used.  For example,
              a 90 nucleotide FASTX query can produce  only  a  30  amino-acid  alignment,  so  a
              scoring  matrix  with 1.33 bits/position is required to produce a 40 bit score. The
              FASTA programs include BLOSUM50 (0.49 bits/pos) and BLOSUM62  (0.58  bits/pos)  but
              can range to MD10 (3.44 bits/position). The variable scoring matrix option searches
              down the list of scoring matrices to find one with information content high  enough
              to produce a 40 bit alignment score.

       -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://ftp.ncbi.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 - [t]fastx36 and [t]fasty36 support the BLAST tranlation tables.
              See http://www.ncbi.nih.gov/htbin-post/Taxonomy/wprintgc?mode=c/.

       -T #   (threaded, parallel only) number of threads or workers to use (on Linux/MacOS/Unix,
              the  default  is  to use as many processors as are available; on Windows systems, 2
              processors are used).

       -U     Do RNA sequence comparisons: treat 'T' as 'U', allow G:U base pairs (by scoring "G-
              A" and "T-C" as score(G:G)-3).  Search only one strand.

       -V "?$%*"
              Allow  special  annotation  characters in query sequence.  These characters will be
              displayed in the alignments on the coordinate number line.

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

       -W # context length (default is 1/2 of line width -w) for alignment,
              like fasta and ssearch, that provide additional sequence context.

       -X extended options.  Less used options. Other options include
              -XB, -XM4G, -Xo, -Xx, and -Xy; see fasta_guide.pdf.

       -z 1, 2, 3, 4, 5, 6
              Specify the statistical calculation. Default is -z 1 for local similarity searches,
              which  uses  regression  against the length of the library sequence. -z -1 disables
              statistics.  -z 0 estimates significance without normalizing for  sequence  length.
              -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 21, 22, 24, 25, 26
              compute two E()-values.  The standard (library-based) E()-value  is  calculated  in
              the standard way (-z 1, 2, etc), but a second E2() value is calculated by shuffling
              the high-scoring sequences (those with E()-values less than  the  threshold).   For
              "average"  composition  proteins,  these  two estimates will be similar (though the
              best-shuffle estimates are  always  more  conservative).   For  biased  composition
              proteins,  the  two  estimates may differ by 100-fold or more.  A second -z option,
              e.g. -z "21 2", specifies the estimation method for the  best-shuffle  E2()-values.
              Best-shuffle  E2()-values approximate the estimates given by PRSS (or in a pairwise
              SSEARCH).

       -Z db_size
              Set the apparent database size used for expectation value  calculations  (used  for
              protein/protein FASTA and SSEARCH, and for [T]FASTX/Y).

Reading sequences from STDIN

       The  FASTA  programs  can accept a query sequence from the unix "stdin" data stream.  This
       makes it much easier to use fasta36 and its relatives as part of a WWW page.  To  indicate
       that  stdin  is to be used, use "@" as the query sequence file name.  "@" can also be used
       to specify a subset of the query sequence to be used, e.g:

     cat query.aa | fasta36 @: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 and assumes
       protein comparisons by default; the '-n' option is required for DNA for STDIN queries.

Environment variables:

       FASTLIBS
              location of library choice file (-l FASTLIBS)

       SRCH_URL1, SRCH_URL2
              format strings used to define options 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

       Version: $ Id: $ Revision: $Revision: 210 $

                                            fasta36/ssearch36/[t]fast[x,y]36/lalign36    1(local)