xenial (1) megablast.1.gz

Provided by: blast2_2.2.26.20120620-10_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/>.