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

source code

Definitions for interacting with BLAST related applications.

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

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]
  _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.
  NcbideltablastCommandline
Create a commandline for the NCBI BLAST+ program deltablast (for proteins).
Functions [hide private]
 
_test()
Run the Bio.Blast.Applications module's doctests.
source code
Variables [hide private]
  __package__ = 'Bio.Blast'