.TH BLASTCL3 1 2016-09-01 NCBI "NCBI Tools User's Manual"
.SH NAME
blastcl3 \- Basic Local Alignment Search Tool client
.SH SYNOPSIS
.B blastcl3
[\|\fB\-\fP\|]
[\|\fB\-A\fP\ \fIN\fP\|]
[\|\fB\-C\fP\ \fIx\fP\|]
[\|\fB\-D\fP\ \fIN\fP\|]
[\|\fB\-E\fP\ \fIN\fP\|]
[\|\fB\-F\fP\ \fIstr\fP\|]
[\|\fB\-G\fP\ \fIN\fP\|]
[\|\fB\-I\fP\|]
[\|\fB\-J\fP\|]
[\|\fB\-K\fP\ \fIN\fP\|]
[\|\fB\-L\fP\ \fIstart,stop\fP\|]
[\|\fB\-M\fP\ \fIstr\fP\|]
[\|\fB\-O\fP\ \fIfilename\fP\|]
[\|\fB\-Q\fP\ \fIN\fP\|]
[\|\fB\-R\fP\|]
[\|\fB\-S\fP\|]
[\|\fB\-T\fP\|]
[\|\fB\-U\fP\|]
[\|\fB\-W\fP\ \fIN\fP\|]
[\|\fB\-X\fP\ \fIN\fP\|]
[\|\fB\-Y\fP\ \fIX\fP\|]
[\|\fB\-Z\fP\ \fIN\fP\|]
[\|\fB\-a\fP\ \fIN\fP\|]
[\|\fB\-b\fP\ \fIN\fP\|]
[\|\fB\-d\fP\ \fIstr\fP\|]
[\|\fB\-e\fP\ \fIX\fP\|]
[\|\fB\-f\fP\ \fIX\fP\|]
[\|\fB\-g\ F\fP\|]
[\|\fB\-i\fP\ \fIfilename\fP\|]
[\|\fB\-m\fP\ \fIN\fP\|]
[\|\fB\-n\fP\|]
[\|\fB\-o\fP\ \fIfilename\fP\|]
\fB\-p\fP\ \fIstr\fP
[\|\fB\-q\fP\ \fIN\fP\|]
[\|\fB\-r\fP\ \fIN\fP\|]
[\|\fB\-s\fP\|]
[\|\fB\-t\fP\ \fIN\fP\|]
[\|\fB\-u\fP\ \fIstr\fP\|]
[\|\fB\-v\fP\ \fIN\fP\|]
[\|\fB\-w\fP\ \fIN\fP\|]
[\|\fB\-y\fP\ \fIX\fP\|]
[\|\fB\-z\fP\ \fIX\fP\|]
.SH DESCRIPTION
\fBblastcl3\fP 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.
.PP
It supports multiple types of comparison, governed by the \fB\-p\fP
("program") flag:
.IP blastp 12
compares an amino acid query sequence against a protein sequence
database.
.IP blastn 12
compares a nucleotide query sequence against a nucleotide sequence
database.
.IP blastx 12
compares the six-frame conceptual translation products of a nucleotide
query sequence (both strands) against a protein sequence database.
.IP psitblastn 12
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.
.IP tblastn 12
compares a protein query sequence against a nucleotide sequence
database dynamically translated in all six reading frames (both
strands).
.IP tblastx 12
compares the six-frame translations of a nucleotide query sequence
against the six-frame translations of a nucleotide sequence database.
.SH OPTIONS
A summary of options is included below.
.TP
\fB\-\fP
Print usage message
.TP
\fB\-A\fP\ \fIN\fP
Multiple Hits window size; generally defaults to 0 (for single-hit
extensions), but defaults to 40 when using discontiguous templates.
.TP
\fB\-C\fP\ \fIX\fP
Use composition-based statistics for blastp or tblastn:
.RS
.PD 0
.IP "T, t, D, or d"
Default (equivalent to \fB1\fP)
.IP "0, F, or f"
No composition-based statistics
.IP 1
Composition-based statistics as in \fINAR\fP 29:2994-3005, 2001
.IP 2
Composition-based score adjustment as in \fIBioinformatics\fP 21:902-911,
2005, conditioned on sequence properties
.IP 3
Composition-based score adjustment as in \fIBioinformatics\fP 21:902-911,
2005, unconditionally
.PD
.RE
.RS
When enabling statistics in blastall, blastall_old, or blastcl3 (\fIi.e.\fP,
not \*(bx), appending \fBu\fP (case-insensitive) to the mode enables
use of unified p-values combining alignment and compositional p-values
in round 1 only.
.RE
.TP
\fB\-D\fP\ \fIN\fP
Translate sequences in the database according to genetic code \fIN\fP
in /usr/share/ncbi/data/gc.prt (default is 1; only applies to tblast*)
.TP
\fB\-E\fP\ \fIN\fP
Extending a gap costs \fIN\fP (\-1 invokes default behavior)
.TP
\fB\-F\fP\ \fIstr\fP
Filter options for DUST or SEG (default is \fBT\fP)
.TP
\fB\-G\fP\ \fIN\fP
Opening a gap costs \fIN\fP (\-1 invokes default behavior)
.TP
\fB\-I\fP
Show GIs in deflines
.TP
\fB\-J\fP
Believe the query defline
.TP
\fB\-K\fP\ \fIN\fP
Number of best hits from a region to keep.
Off by default.
If used a value of 100 is recommended.
.TP
\fB\-L\fP\ \fIstart,stop\fP
Location on query sequence.
.TP
\fB\-M\fP\ \fIstr\fP
Use matrix \fIstr\fP (default = BLOSUM62)
.TP
\fB\-O\fP\ \fIfilename\fP
Write (ASN.1) sequence alignments to \fIfilename\fP..
.TP
\fB\-P\fP\ \fIN\fP
Set to 1 for single-hit mode or 0 for multiple-hit mode (default).
Does not apply to blastn.
.TP
\fB\-Q\fP\ \fIN\fP
Translate query according to genetic code \fIN\fP in
/usr/share/ncbi/data/gc.prt (default is 1)
.TP
\fB\-R\fP
RPS Blast search
.TP
\fB\-S\fP\ \fIN\fP
Query strands to search against database for blastn, blastx, tblastx:
.RS
.PD 0
.IP 1
top
.IP 2
bottom
.IP 3
both (default)
.PD
.RE
.TP
\fB\-T\fP
Produce HTML output
.TP
\fB\-U\fP
Use lower case filtering for the query sequence
.TP
\fB\-W\fP\ \fIN\fP
Use words of size \fIN\fP (length of best perfect match; zero invokes
default behavior -- 11 for blastn [28 in MegaBlast mode], 3 otherwise).
.TP
\fB\-X\fP\ \fIN\fP
X dropoff value for gapped alignment (in bits) (zero invokes default
behavior, which varies with "program": 30 for blastn [20 in MegaBlast
mode], 0 for tblastx, and 15 for everything else.)
.TP
\fB\-Y\fP\ \fIX\fP
Effective length of the search space (use zero for the real size)
.TP
\fB\-Z\fP\ \fIN\fP
X dropoff value for final [dynamic programming?] gapped alignment in
bits (default is 50 for blastn, 0 for tblastx, 25 for others)
.TP
\fB\-a\fP\ \fIN\fP
Number of threads to use (default is one)
.TP
\fB\-b\fP\ \fIN\fP
Number of database sequences to show alignments for (B) (default is 250)
.TP
\fB\-d\fP\ \fIstr\fP
Database to use (default is nr)
.TP
\fB\-e\fP\ \fIX\fP
Expectation value (E) (default = 10.0)
.TP
\fB\-f\fP\ \fIX\fP
Threshold for extending hits, default if zero: 0 for blastn,
11 for blastp, 12 for blastx, and 13 for tblastn and tblastx.
.TP
\fB\-g\ F\fP
Do not perform gapped alignment (N/A for tblastx)
.TP
\fB\-i\fP\ \fIfilename\fP
Read query sequence or set from \fIfilename\fP (default is stdin)
.TP
\fB\-m\fP\ \fIN\fP
alignment view options:
.RS
.PD 0
.IP 0
pairwise (default)
.IP 1
query-anchored showing identities
.IP 2
query-anchored, no identities
.IP 3
flat query-anchored, show identities
.IP 4
flat query-anchored, no identities
.IP 5
query-anchored, no identities and blunt ends
.IP 6
flat query-anchored, no identities and blunt ends
.IP 7
XML Blast output
.IP 8
tabular
.IP 9
tabular with comment lines
.IP 10
ASN.1 text
.IP 11
ASN.1 binary
.PD
.RE
.TP
\fB\-n\fP
MegaBlast search
.TP
\fB\-o\fP\ \fIfilename\fP
Write final alignment report to \fIfilename\fP rather than stdout
.TP
\fB\-p\fP\ \fIstr\fP
Use the "program" (comparison type) \fIstr\fP.  The \fBDESCRIPTION\fP
section covers this option in more detail.
.TP
\fB\-q\fP\ \fIN\fP
Penalty for a nucleotide mismatch (blastn only) (default = \-3)
.TP
\fB\-r\fP\ \fIN\fP
Reward for a nucleotide match (blastn only) (default = \-10)
.TP
\fB\-s\fP
Compute locally optimal Smith-Waterman alignments (only available in gapped
tblastn mode).
.TP
\fB\-t\fP\ \fIN\fP
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.)
.TP
\fB\-u\fP\ \fIstr\fP
Restrict search of database to results of Entrez2 lookup
.TP
\fB\-v\fP\ \fIN\fP
Number of one-line descriptions to show (V) (default = 500)
.TP
\fB\-w\fP\ \fIN\fP
Frame shift penalty (OOF algorithm for blastx)
.TP
\fB\-y\fP\ \fIX\fP
X dropoff for ungapped extensions in bits (0.0 invokes default
behavior: 20 for blastn [10 in MegaBlast mode], 7 otherwise).
.TP
\fB\-z\fP\ \fIN\fP
Effective length of the database (use zero for the real size)
.SH AUTHOR
The National Center for Biotechnology Information.
.SH SEE ALSO
.ad l
<http://blast.ncbi.nlm.nih.gov/>.