org.strbio.app
Class BlastProtein

java.lang.Object
  org.strbio.app.BlastProtein

public class BlastProtein
extends java.lang.Object

Run Blast on a protein (or set).

  Version 3.1, 3/27/03 - added -max, -e options
  Version 3.0, 2/21/02 - added -savematrix, -saveout, -restore,
    savetxt options, removed -m option
  Version 2.8, 12/2/01 - added -h option
  Version 2.7, 10/19/01 - added tblastn option
  Version 2.6, 8/6/1 - added -skip N, changed old -skip to -skipdone
    added -nosw to not do S/W alignment for psiblast, as this sometimes
    causes psiblast 2.2.1 to hang!
  Version 2.5, 3/26/1 - made default db nrfilt; changed docs
  Version 2.42, 5/2/00 - added -size restriction
  Version 2.41, 4/24/00 - added -db2, -keep options
  Version 2.4, 4/21/00 - added -psi2 option, -db option
  Version 2.31, 4/11/00 - updated to use new NCBI programs
  Version 2.3, 4/6/00 - added -skip option
  Version 2.21, 10/14/99 - uses Enumeration reader, fixing bug where
    chain ID of PDB files was lost.
  Version 2.2, 3/22/99 - added -net blast options
  Version 2.11, 3/1/99 - warns if no proteins found.
  Version 2.1, 2/17/99 - does blasting one protein at a time, in
    case something crashes.  Also saves on memory.
  Version 2.03, 2/17/99 - added YAPF format, no longer have to save matrices
  Version 2.02, 1/29/99 - can save PSIBlast matrices with -m
  Version 2.01, 1/20/99 - added some more BLAST servers.
  Version 2.0, 1/19/99 - can get BLAST from a variety of sources,
  including over the net or locally.
  Version 1.01, 11/30/98 - moved most routines to ProteinSet class.
  Version 1.0, 11/17/98 - original version
  

Version:

3.1, 3/27/03

Author:

JMC

See Also:

BlastNCBI

Field Summary

static java.lang.String

VERSION

Constructor Summary

BlastProtein()

Method Summary

static void

main(java.lang.String[] argv)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

VERSION

public static final java.lang.String VERSION

See Also:

Constant Field Values

Constructor Detail

BlastProtein

public BlastProtein()

Method Detail

main

public static final void main(java.lang.String[] argv)