Package Bio :: Package Blast :: Module Applications
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Module Applications

source code

Definitions for interacting with BLAST related applications.

Obsolete wrappers for the old/classic NCBI BLAST tools (written in C):

- FastacmdCommandline
- BlastallCommandline
- BlastpgpCommandline
- RpsBlastCommandline

Wrappers for the new NCBI BLAST+ tools (written in C++):

- NcbiblastpCommandline - Protein-Protein BLAST
- NcbiblastnCommandline - Nucleotide-Nucleotide BLAST
- NcbiblastxCommandline - Translated Query-Protein Subject BLAST
- NcbitblastnCommandline - Protein Query-Translated Subject BLAST
- NcbitblastxCommandline - Translated Query-Protein Subject BLAST
- NcbipsiblastCommandline - Position-Specific Initiated BLAST
- NcbirpsblastCommandline - Reverse Position Specific BLAST
- NcbirpstblastnCommandline - Translated Reverse Position Specific BLAST
- NcbiblastformatterCommandline - Convert ASN.1 to other BLAST output formats

For further details, see:

Camacho et al. BLAST+: architecture and applications
BMC Bioinformatics 2009, 10:421
doi:10.1186/1471-2105-10-421

Classes [hide private]
  FastacmdCommandline
Create a commandline for the fasta program from NCBI (OBSOLETE).
  _BlastCommandLine
Base Commandline object for (classic) NCBI BLAST wrappers (PRIVATE).
  _BlastAllOrPgpCommandLine
Base Commandline object for NCBI BLAST wrappers (PRIVATE).
  BlastallCommandline
Create a commandline for the blastall program from NCBI (OBSOLETE).
  BlastpgpCommandline
Create a commandline for the blastpgp program from NCBI (OBSOLETE).
  RpsBlastCommandline
Create a commandline for the classic rpsblast program from NCBI (OBSOLETE).
  _NcbibaseblastCommandline
Base Commandline object for (new) NCBI BLAST+ wrappers (PRIVATE).
  _NcbiblastCommandline
Base Commandline object for (new) NCBI BLAST+ wrappers (PRIVATE).
  _Ncbiblast2SeqCommandline
Base Commandline object for (new) NCBI BLAST+ wrappers (PRIVATE).
  _NcbiblastMain2SeqCommandline
Base Commandline object for (new) NCBI BLAST+ wrappers (PRIVATE).
  NcbiblastpCommandline
Create a commandline for the NCBI BLAST+ program blastp (for proteins).
  NcbiblastnCommandline
Wrapper for the NCBI BLAST+ program blastn (for nucleotides).
  NcbiblastxCommandline
Wrapper for the NCBI BLAST+ program blastx (nucleotide query, protein database).
  NcbitblastnCommandline
Wrapper for the NCBI BLAST+ program tblastn.
  NcbitblastxCommandline
Wrapper for the NCBI BLAST+ program tblastx.
  NcbipsiblastCommandline
Wrapper for the NCBI BLAST+ program psiblast.
  NcbirpsblastCommandline
Wrapper for the NCBI BLAST+ program rpsblast.
  NcbirpstblastnCommandline
Wrapper for the NCBI BLAST+ program rpstblastn.
  NcbiblastformatterCommandline
Wrapper for the NCBI BLAST+ program blast_formatter.
Functions [hide private]
 
_test()
Run the Bio.Blast.Applications module's doctests.
source code
Variables [hide private]
  __package__ = 'Bio.Blast'