Provided by: blast2_2.2.25.20110713-3ubuntu2_amd64 bug

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/>.