Man Linux: Main Page and Category List

NAME

       bl2seq,  blast2,  blastall,  blastall_old,  blastcl3, blastpgp, impala,
       megablast, rpsblast, seedtop - Basic Local Alignment Search Tool

SYNOPSIS

       bl2seq  [-]  [-A]  [-D N]  [-E N]  [-F str]  [-G N]   [-I "start stop"]
       [-J "start stop"]  [-M str]  [-S N] [-T] [-U] [-V] [-W N] [-X N] [-Y X]
       [-a filename]  [-d N]  [-e X]  [-g F]  -i filename   -j filename   [-m]
       [-o filename] -p str [-q N] [-r N] [-t N]

       blast2   [-]   [-B N]   [-D N]   [-C x]  [-E N]  [-F str]  [-G N]  [-H]
       [-I "start stop"] [-J "start stop"] [-K N] [-L]  [-M str]  [-N]  [-P X]
       [-Q N]  [-R]  [-S N]  [-T N]  [-W N] [-X N] [-Y X] [-Z N] [-a N] [-b N]
       [-c] [-d str] [-e X] [-f X]  [-g]  [-h N]  [-i filename]  [-j filename]
       [-k str]  [-m N]  [-n]  [-o filename]  -p str [-q N] [-r N] [-s] [-t N]
       [-u] [-v N] [-w N] [-y N] [-z N]

       blastall [-] [-A N] [-B N] [-C x] [-D N] [-E N]  [-F str]  [-G N]  [-I]
       [-J]   [-K N]  [-L start,stop]  [-M str]  [-O filename]  [-P N]  [-Q N]
       [-R filename] [-S] [-T] [-U] [-V] [-W N] [-X N]  [-Y X]  [-Z N]  [-a N]
       [-b N] [-d str] [-e X] [-f X] [-g F] [-i filename] [-l str] [-m N] [-n]
       [-o filename] -p str [-q N] [-r N] [-s]  [-t N]  [-v N]  [-w N]  [-y X]
       [-z X]

       blastall_old  [-]  [-A N]  [-B N]  [-C x] [-D N] [-E N] [-F str] [-G N]
       [-I] [-J] [-K N] [-L start,stop] [-M str] [-O filename]  [-P N]  [-Q N]
       [-R filename]  [-S] [-T] [-U] [-W N] [-X N] [-Y X] [-Z N] [-a N] [-b N]
       [-d str]  [-e X]  [-f X]  [-g F]  [-i filename]  [-l str]  [-m N]  [-n]
       [-o filename]  -p str  [-q N]  [-r N]  [-s] [-t N] [-v N] [-w N] [-y X]
       [-z X]

       blastcl3 [-] [-A N] [-C x] [-D N]  [-E N]  [-F str]  [-G N]  [-I]  [-J]
       [-K N]  [-L start,stop]  [-M str]  [-O filename]  [-Q N] [-R] [-S] [-T]
       [-U] [-W N] [-X N] [-Y X] [-Z N] [-a N] [-b N] [-d str]  [-e X]  [-f X]
       [-g F]  [-i filename]  [-m N]  [-n]  [-o filename] -p str [-q N] [-r N]
       [-s] [-t N] [-u str] [-v N] [-w N] [-y X] [-z X]

       blastpgp [-] [-A N] [-B filename] [-C filename] [-E N]  [-F  T]  [-G N]
       [-H N]  [-I]  [-J]  [-K N]  [-L N] [-M str] [-N X] [-O filename] [-P N]
       [-Q filename] [-R filename]  [-S N]  [-T]  [-U]  [-W N]  [-X N]  [-Y X]
       [-Z N] [-a N] [-b N] [-c N] [-d str] [-e X] [-f N] [-h X] [-i filename]
       [-j N] [-k filename] [-l str] [-m N] [-o filename] [-p str] [-q N] [-s]
       [-t N[u]] [-u N] [-v N] [-y X] [-z N]

       impala [-] [-E N] [-F str] [-G N] [-H] [-I] [-J] [-M str] [-O filename]
       [-P filename] [-a N] [-b N] [-c N] [-d str] [-e X] [-h X] [-i filename]
       [-j N] [-m N] [-o filename] [-v N] [-y X] [-z N]

       megablast  [-]  [-A N]  [-D N]  [-E N] [-F str] [-G N] [-H N] [-I] [-J]
       [-L start,stop] [-M N] [-N N] [-O filename] [-P N]  [-Q filename]  [-R]
       [-S N]  [-T]  [-U]  [-V]  [-W N]  [-X N]  [-Y X]  [-Z N]  [-a N] [-b N]
       [-d str]  [-e X]  [-f]  [-g F]  [-i filename]  [-l str]   [-m N]   [-n]
       [-o filename] [-p X] [-q N] [-r N] [-t N] [-s N] [-v N] [-y N] [-z X]

       rpsblast  [-]  [-F str]  [-I] [-J] [-L start,stop] [-N X] [-O filename]
       [-P N] [-T] [-U] [-X N] [-Y X] [-Z N] [-a N] [-b N] -d filename  [-e X]
       [-i filename]  [-l filename]  [-m N] [-o filename] [-p F] [-v N] [-y X]
       [-z N]

       seedtop [-] [-C N] [-D N] [-E N] [-F] [-G N] [-I] [-J] [-K N]  [-M str]
       [-O filename]   [-S N]   [-X N]   [-d str]  [-e X]  [-f]  [-i filename]
       [-k filename] [-o filename] [-p str] [-q N] [-r N]

DESCRIPTION

       This  manual  page  documents  briefly  the  commands  bl2seq,   blast,
       blastall, blastcl3, blastpgp, impala, megablast, rpsblast, and seedtop.
       These commands are documented together  because  they  have  a  lot  of
       common options.

       bl2seq  performs  a  comparison  between two sequences using either the
       blastn or blastp algorithm.  Both sequences must be either  nucleotides
       or proteins.

       blast2  compares a sequence against either a local database or a second
       sequence; it incorporates most of the functionality of both bl2seq  and
       blastall, but uses a semi-experimental new internal engine.

       blastall and blastall_old find the best matches in a local database for
       a sequence.  blastall uses a newer engine than blastall_old by default,
       but  supports  using  the  older  engine as well (when invoked with the
       option -V F).

       blastcl3 accesses the newest NCBI BLAST search  engine  (version  2.0).
       The software behind BLAST version 2.0 was written from scratch to allow
       BLAST to handle the new challenges posed by the sequence  databases  in
       the coming years.  Updates to this software will continue in the coming
       years.

       blastpgp performs gapped blastp searches and can  be  used  to  perform
       iterative searches in psi-blast and phi-blast mode.

       impala  searches  a database of score matrices, prepared by copymat(1),
       producing BLAST-like output.

       megablast  uses  the  greedy  algorithm  of  Webb  Miller  et  al.  for
       nucleotide  sequence  alignment search and concatenates many queries to
       save time spent scanning the database. This program  is  optimized  for
       aligning  sequences  that  differ slightly as a result of sequencing or
       other similar "errors". It is up to 10 times faster  than  more  common
       sequence  similarity  programs  and  therefore  can  be used to swiftly
       compare two large sets of sequences against each other.

       rpsblast (Reverse  PSI-BLAST)  searches  a  query  sequence  against  a
       database  of profiles.  This is the opposite of PSI-BLAST that searches
       a profile  against  a  database  of  sequences,  hence  the  ‘Reverse’.
       rpsblast  uses  a  BLAST-like algorithm, finding single- or double-word
       hits and then performing  an  ungapped  extension  on  these  candidate
       matches.    If   a  sufficiently  high-scoring  ungapped  alignment  is
       produced, a gapped extension is performed and those (gapped) alignments
       with  sufficiently low expect value are reported.  This procedure is in
       contrast to IMPALA that performs a Smith-Waterman  calculation  between
       the  query  and  each profile, rather than using a word-hit approach to
       identify matches that should be extended.

       seedtop answers two relatively simple questions:
       1.     Given a sequence and a  database  of  patterns,  which  patterns
              occur in the sequence and where?
       2.     Given a pattern and a sequence database, which sequences contain
              the pattern and where?

       Some of these commands support multiple types of  comparison,  governed
       by the -p ("program") flag:

       blastp      compares  an  amino  acid  query sequence against a protein
                   sequence database.

       blastn      compares a nucleotide query sequence against  a  nucleotide
                   sequence database.

       blastx      compares the six-frame conceptual translation products of a
                   nucleotide query sequence (both strands) against a  protein
                   sequence  database.   For  bl2seq, the nucleotide should be
                   the first sequence given.

       psitblastn  compares a protein  query  sequence  against  a  nucleotide
                   sequence database dynamically translated in all six reading
                   frames (both strands)  using  a  position  specific  matrix
                   created by PSI-BLAST.

       tblastn     compares  a  protein  query  sequence  against a nucleotide
                   sequence database dynamically translated in all six reading
                   frames  (both  strands).  For bl2seq, the nucleotide should
                   be the second sequence given.

       tblastx     compares the six-frame translations of a  nucleotide  query
                   sequence against the six-frame translations of a nucleotide
                   sequence database.

OPTIONS

       A summary of options is included below.

       -      Print usage message

       -A (bl2seq)
              Input sequences in the form of accession.version

       -A N (blastall, blastall_old, blastcl3, blastpgp, megablast)
              Multiple Hits window size; generally defaults to 0 (for  single-
              hit  extensions),  but  defaults  to 40 when using discontiguous
              templates.

       -B N (blast2)
              Produce on-the-fly output:
              0      none (default)
              1      table of offsets and quality values
              2      add sequence data
              3      text ASN.1
              4      binary ASN.1

       -B N (blastall, blastall_old)
              Number of concatenated queries, in blastn or tblastn mode

       -B filename (blastpgp)
              Input Alignment File for PSI-BLAST Restart

       -C X (blast2, blastall, blastall_old, blastcl3)
              Use composition-based statistics for blastp or tblastn:
              T, t, D, or d
                     Default (equivalent to 1 for blast2 and blastall_old  and
                     to 2 for blastall and blastcl3)
              0, F, or f
                     No composition-based statistics
              1      Composition-based statistics as in NAR 29:2994-3005, 2001
              2      Composition-based score adjustment as  in  Bioinformatics
                     21:902-911, 2005, conditioned on sequence properties
              3      Composition-based  score  adjustment as in Bioinformatics
                     21:902-911, 2005, unconditionally
              When enabling statistics in blastall, blastall_old, or  blastcl3
              (i.e.,  not  blast2), appending u (case-insensitive) to the mode
              enables  use  of  unified  p-values  combining   alignment   and
              compositional p-values in round 1 only.

       -C filename (blastpgp)
              Output File for PSI-BLAST Checkpointing

       -C N (seedtop)
              Score only or not (default = 1)

       -D N (bl2seq)
              Output format:
              0      traditional (default)
              1      tabular

       -D N (blast2, blastall, blastall_old, blastcl3)
              Translate  sequences in the database according to genetic code N
              in /usr/share/ncbi/data/gc.prt (default is 1;  only  applies  to
              tblast*)

       -D N (megablast)
              Type of output:
              0      alignment endpoints and score
              1      all ungapped segments endpoints
              2      traditional BLAST output (default)
              3      tab-delimited one line format
              4      incremental text ASN.1
              5      incremental binary ASN.1

       -D N (seedtop)
              Cost decline to align (default = 99999)

       -E N (bl2seq, blastcl3, megablast)
              Extending a gap costs N (-1 invokes default behavior)

       -E N (blast2, blastall, blastall_old)
              Extending a gap costs N (-1 invokes default behavior: non-affine
              if greedy, 2 otherwise)

       -E N (blastpgp, impala, seedtop)
              Extending a gap costs N (default is 1)

       -F str (bl2seq, blast2, blastall, blastall_old, blastpgp,
              blastcl3, impala, megablast, rpsblast) Filter options  for  DUST
              or   SEG;   defaults   to   T   for  bl2seq,  blast2,  blastall,
              blastall_old, blastcl3, and megablast, and to  F  for  blastpgp,
              impala, and rpsblast.

       -F (seedtop)
              Filter sequence with SEG.

       -G N (bl2seq, blastcl3, megablast)
              Opening a gap costs N (-1 invokes default behavior)

       -G N (blast2, blastall, blastall_old)
              Opening  a  gap costs N (-1 invokes default behavior: non-affine
              if greedy, 5 if using dynamic programming)

       -G N (blastpgp, impala, seedtop)
              Opening a gap costs N (default is 11)

       -H (blast2)
              Produce HTML output

       -H N (blastpgp)
              End of required region in query (-1 indicates end of query)

       -H (impala)
              Print help (different from usage message)

       -H N (megablast)
              Maximal number of HSPs to save per database sequence (default is
              0, unlimited)

       -I "start stop" (bl2seq, blast2)
              Location  on  first  (query)  sequence  (applies  only  if  file
              specified with -i contains a single sequence)

       -I (blastall, blastall_old, blastcl3, blastpgp, impala, megablast,
              rpsblast, seedtop) Show GIs in deflines

       -J "start stop" (bl2seq, blast2)
              Location on second (subject)  sequence  (applies  only  if  file
              specified with -j contains a single sequence)

       -J (blastall, blastall_old, blastcl3, blastpgp, impala, megablast,
              rpsblast, seedtop) Believe the query defline

       -K N (blast2, blastall, blastall_old, blastcl3, blastpgp)
              Number  of best hits from a region to keep.  Off by default.  If
              used a value of 100 is recommended.  Very high values of  -v  or
              -b are also suggested.

       -K N (seedtop)
              Internal hit buffer size multiplier (wrt query length; default =
              2)

       -L (blast2)
              Use (classical Mega BLAST) lookup table with width 12

       -L start,stop (blastall, blastall_old, blastcl3, megablast,
              rpsblast) Location on query sequence (for rpsblast,  only  valid
              in blastp mode)

       -M str (bl2seq, blast2, blastall, blastall_old, blastcl3,
              blastpgp, impala, seedtop) Use matrix str (default = BLOSUM62)

       -M N (megablast)
              Maximal  total  length of queries for a single search (default =
              5000000)

       -N (blast2)
              Show only accessions for sequence IDs in tabular output

       -N X (blastpgp, rpsblast)
              Number of bits to trigger gapping (default = 22.0)

       -N N (megablast)
              Type of a discontiguous word template:
              0      coding (default)
              1      optimal
              2      two simultaneous

       -O filename (blastall, blastall_old, blastcl3,
              blastpgp, impala, megablast, rpsblast,  seedtop)  Write  (ASN.1)
              sequence  alignments  to  filename;  only  valid  for  blastpgp,
              impala, rpsblast, and  seedtop  with  -J,  and  only  valid  for
              megablast with -D2.

       -P X (blast2)
              Identity percentage cut-off

       -P N (blastall, blastall_old, blastcl3, blastpgp, rpsblast)
              Set  to  1  for  single-hit  mode  or  0  for  multiple-hit mode
              (default).  Does not apply to blastn.

       -P filename (impala)
              Read matrix profiles from database filename

       -P N (megablast)
              Maximal number of positions for a hash value (set to 0 [default]
              to ignore)

       -Q N (blast2, blastall, blastall_old, blastcl3)
              Translate    query    according    to    genetic   code   N   in
              /usr/share/ncbi/data/gc.prt (default is 1)

       -Q filename (blastpgp)
              Output File for PSI-BLAST Matrix in ASCII

       -Q filename (megablast)
              Masked query output; requires -D 2

       -R (blast2)
              Compute locally optimal Smith-Waterman alignments.  (This option
              is only available for gapped tblastn.)

       -R filename (blastall, blastall_old)
              Read PSI-TBLASTN checkpoint file filename

       -R (blastcl3)
              RPS Blast search

       -R filename (blastpgp)
              Input File for PSI-BLAST Restart

       -R (megablast)
              Report the log information at the end of output

       -S N (bl2seq, blast2, blastall, blastall_old, blastcl3,
              megablast)  Query strands to search against database for blastn,
              blastx, tblastx:
              1      top
              2      bottom
              3      both (default)

       -S N (blastpgp)
              Start of required region in query (default = 1)

       -S N (seedtop)
              Cutoff cost (default = 30)

       -T (bl2seq, blastall, blastall_old, blastcl3, blastpgp, megablast,
              rpsblast) Produce HTML output

       -T N (blast2)
              Type of a discontiguous word template:
              0      coding (default)
              1      optimal
              2      two simultaneous

       -U (bl2seq, blastall, blastall_old, blastcl3, blastpgp, megablast,
              rpsblast) Use lower case filtering for the query sequence

       -V (bl2seq, blastall, megablast)
              Force use of legacy engine

       -V (blast2)
              Use variable word size approach to database scanning

       -W N (bl2seq, blast2, blastall, blastall_old, blastcl3,
              blastpgp, megablast, rpsblast) Use words of size  N  (length  of
              best  perfect  match; zero invokes default behavior, except with
              megablast, which defaults to 28, and blastpgp, which defaults to
              3.   The  default  values  for  the  other  commands  vary  with
              "program": 11 for blastn, 28 for megablast, and 3 for everything
              else.)

       -X N (bl2seq, blast2, blastall, blastall_old, blastcl3,
              blastpgp,  megablast,  rpsblast,  seedtop)  X  dropoff value for
              gapped alignment  (in  bits)  (zero  invokes  default  behavior,
              except  with  megablast,  which defaults to 20, and rpsblast and
              seedtop, which default to 15.  The default values for the  other
              commands vary with "program": 30 for blastn, 20 for megablast, 0
              for tblastx, and 15 for everything else.)

       -Y X (bl2seq, blast2, blastall, blastall_old, blastcl3,
              blastpgp, megablast, rpsblast) Effective length  of  the  search
              space (use zero for the real size)

       -Z N (blast2, blastall, blastall_old, blastcl3, blastpgp,
              megablast,   rpsblast)   X  dropoff  value  for  final  [dynamic
              programming?] gapped alignment  in  bits  (default  is  100  for
              blastn and megablast, 0 for tblastx, 25 for others)

       -a filename (bl2seq)
              Write text ASN.1 output to filename

       -a N (blast2, blastall, blastall_old, blastcl3, blastpgp,
              impala,  megablast,  rpsblast) Number of threads to use (default
              is one)

       -b N (blast2, blastall, blastall_old, blastcl3, blastpgp,
              impala, megablast, rpsblast) Number  of  database  sequences  to
              show alignments for (B) (default is 250)

       -c (blast2)
              Mask lower case

       -c N (impala)
              Constant in pseudocounts for multipass version; 0 (default) uses
              entropy method; otherwise a value near 30 is recommended

       -c N (impala)
              Constant in pseudocounts for multipass version (default is 10)

       -d N (bl2seq)
              Use theoretical DB size of N (zero stands for the real size)

       -d str (blast2, blastall, blastall_old, blastcl3, blastpgp,
              impala, megablast, seedtop) Database to use (default is  nr  for
              all  executables  except  blast2,  which requires a second FASTA
              sequence if this is not set)

       -d filename (rpsblast)
              RPS BLAST Database

       -e X   Expectation value (E) (default = 10.0)

       -f X (blast2, blastall, blastall_old, blastcl3)
              Threshold for extending hits, default if zero: 0 for blastn  and
              megablast,  11  for blastp, 12 for blastx, and 13 for tblasn and
              tblastx.

       -f N (blastpgp)
              Threshold for extending hits (default 11)

       -f (megablast)
              Show full IDs in the output (default: only GIs or accessions)

       -f (seedtop)
              Force searching for patterns even if they are too likely

       -g F (bl2seq, blastall, blastall_old, blastcl3)
              Do not perform gapped alignment (N/A for tblastx)

       -g (blast2)
              Use greedy algorithm for gapped extensions

       -g F (megablast)
              Make discontiguous megablast generate words for  every  base  of
              the database (mandatory with the current BLAST engine)

       -h N (blast2)
              Frame  shift  penalty  for out-of-frame gapping (blastx, tblastn
              only; default is zero)

       -h X (blastpgp, impala)
              e-value threshold for inclusion in multipass  model  (default  =
              0.002 for blastpgp, 0.005 for impala)

       -i filename
              Read  (first,  query)  sequence or set from filename (default is
              stdin; not needed for blastpgp if restarting from scoremat)

       -j filename (bl2seq, blast2)
              Read second (subject) sequence or set from filename

       -j N (blastpgp)
              Maximum number of passes to use in multipass version (default  =
              1)

       -k str (blast2)
              Pattern for PHI-BLAST

       -k filename (blastpgp, seedtop)
              Input hit file for PHI-BLAST (default = hit_file)

       -l str (blastall, blastall_old, blastpgp, megablast)
              Restrict search of database to list of GI’s [String]

       -l filename (rpsblast)
              Log messages to filename rather than standard error.

       -m (bl2seq)
              Use Mega Blast for search

       -m N (blast2, blastall, blastall_old, blastcl3, blastpgp,
              impala, megablast, rpsblast) alignment view options:
              0      pairwise (default)
              1      query-anchored showing identities
              2      query-anchored, no identities
              3      flat query-anchored, show identities
              4      flat query-anchored, no identities
              5      query-anchored, no identities and blunt ends
              6      flat query-anchored, no identities and blunt ends
              7      XML Blast output (not available for impala)
              8      tabular (not available for impala)
              9      tabular with comment lines (not available for impala)
              10     ASN.1 text (not available for impala or rpsblast)
              11     ASN.1 binary (not available for impala or rpsblast)

       -n (blast2)
              Show GIs in sequence IDs

       -n (blastall, blastall_old, blastcl3)
              MegaBlast search

       -n (megablast)
              Use  non-greedy  (dynamic  programming) extension for affine gap
              scores

       -o filename
              Write final alignment report to filename rather than stdout

       -p str (bl2seq, blast2, blastall, blastall_old, blastcl3)
              Use  the  "program"  (comparison  type)  str.   The  DESCRIPTION
              section covers this option in more detail.

       -p str (blastpgp)
              program option for PHI-BLAST (default = blastpgp)

       -p X (megablast)
              Identity percentage cut-off (default = 0)

       -p F (rpsblast)
              Query sequence is nucleotide, not protein

       -p str (seedtop)
              program name:
              patmatchp indicates which patterns occur in a sequence
              patternp  indicates which sequences contain a pattern

       -q N (bl2seq, blast2, blastall, blastall_old, blastcl3,
              megablast,  seedtop)  Penalty  for a nucleotide mismatch (blastn
              only) (default = -10 for seedtop, -3 for everything else)

       -q N (blastpgp)
              ASN.1 Scoremat input of checkpoint data:
              0      no scoremat input (default)
              1      restart from ASCII scoremat checkpoint file
              2      restart from binary scoremat checkpoint file

       -r N (bl2seq, blast2, blastall, blastall_old, blastcl3,
              megablast, seedtop) Reward for a nucleotide match (blastn  only)
              (default = 10 for seedtop, -10 for everything else)

       -s (blast2)
              No-op (formerly requested generating words for every base of the
              database)

       -s (blastall, blastall_old, blastcl3, blastpgp)
              Compute  locally   optimal   Smith-Waterman   alignments.    For
              blastall,  blastall_old, and blastcl3, this is only available in
              gapped tblastn mode.

       -s N (megablast)
              Minimal hit score to report (0 for default behavior)

       -t N (bl2seq, blast2, blastall, blastall_old, blastcl3)
              Length of a discontiguous  word  template  (the  largest  intron
              allowed   in  a  translated  nucleotide  sequence  when  linking
              multiple distinct assignments;  default  =  0;  negative  values
              disable linking for blastall, blastall_old, and blastcl3.)

       -t N[u] (blastpgp)
              Composition-based  score  adjustment.   The  first  character is
              interpreted as follows:
              0, F, or f
                     no composition-based statistics
              1      composition-based statistics as in NAR 29:2994-3005, 2001
              2, T, or t
                     composition-based  score  adjustment as in Bioinformatics
                     21:902-911, 2005, conditioned on sequence  properties  in
                     round 1 (default)
              3      composition-based  score  adjustment as in Bioinformatics
                     21:902-911, 2005, unconditionally in round 1

              When composition-based statistics are in use, appending u (case-
              insensitive)  to the argument requests unified p-value combining
              alignment p-value and compositional p-value in round 1 only.

       -t N (megablast)
              Length of a discontiguous word template (contiguous  word  if  0
              [default])

       -u (blast2)
              Do only ungapped alignment (always TRUE for tblastx)

       -u str (blastcl3)
              Restrict search of database to results of Entrez2 lookup

       -u N (blastpgp)
              ASN.1 Scoremat output of checkpoint data:
              0      no scoremat output (default)
              1      output ASCII scoremat checkpoint file (requires -J)
              2      output binary scoremat checkpoint file (requires -J)

       -v N (blast2, blastall, blastall_old, blastcl3, blastpgp,
              impala,  megablast, rpsblast) Number of one-line descriptions to
              show (V) (default = 500)

       -w N (blast2)
              Window size (max. allowed distance between  a  pair  of  initial
              hits; 0 invokes default behavior, -1 turns off multiple hits)

       -w N (blastall, blastall_old, blastcl3)
              Frame shift penalty (OOF algorithm for blastx)

       -y X (blast2, blastall, blastall_old, blastcl3, blastpgp,
              impala, rpsblast) X dropoff for ungapped extensions in bits (0.0
              invokes default behavior: 20 for blastn, 10 for megablast, and 7
              for all others.)

       -y N (megablast)
              X dropoff value for ungapped extension (default is 10)

       -z N (blast2)
              Longest  intron length for uneven gap HSP linking (tblastn only;
              default is 0)

       -z N (blastall, blastall_old, blastcl3, blastpgp, impala,
              megablast, rpsblast) Effective length of the database (use  zero
              for the real size)

BUGS

       This  manual  page  is  long  and  confusing; individual pages might be
       better.

AUTHOR

       The National Center for Biotechnology Information.

SEE ALSO

       blastclust(1), copymat(1), fastacmd(1), formatdb(1), formatrpsdb(1),
       makemat(1), taxblast(1), /usr/share/doc/blast2/blast.html,
       /usr/share/doc/blast2/seedtop.html,
       <http://www.ncbi.nlm.nih.gov/BLAST/>.