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BLAST and PSI-BLAST
in YASARA
BLAST, the basic local alignment search tool,
has become an integral part of virtually all bioinformatics
research[1]. While web servers make access
to BLAST easy, its distribution and tight integration with YASARA
offer a number of advantages:
- The YASARA distribution server at the CMBI
provides BLAST
libraries of SwissProt, UniRef90, PDB and PDBC. 'PDBC'
contains the sequences extracted from the ATOM Coordinate section of
the PDB file, which avoids many pitfalls associated with the normally
used PDB sequence databases (based on the SEQRES record).The PDB and PDBC databases are updated weekly and augmented with quality scores from the PDBFinder2 database. So BLASTing against the PDB will not only yield PDB IDs, but also
information about structural quality, and if there are multiple
structures with the same sequence, the best structure will be ranked
first. This concept also helps template selection in homology modeling.
- The local BLAST libraries are updated fully
automatically
by YASARA.
- The direct integration obviates the need to
first obtain
the sequence of a protein structure, and then copy & paste it to
BLAST. Also Python scripts and Yanaconda macros benefit a lot. The
following example macro runs BLAST for a given protein structure
(interleukin-8), downloads the PDB files of the hits and aligns them
structurally, resulting in the scene shown on the right side:
# Find and structurally align PDB entries with a # similar sequence Clear # Load Interleukin 8 dst = LoadPDB 3il8 # Get a non-redundant list of BLAST hits in the PDB: # Evalue1, PDB ID1, molecule1, Evalue2, PDB ID2… resultlist() = BlastObj (dst),Database=PDBnr for i=1 to count resultlist step 3 # (Down)load the PDB file src = LoadPDB (resultlist(i+1)),Model=1,Download=Yes # Keep only the molecule reported by BLAST DelMol not (resultlist(i+2)) and Obj (src) # Make a structural alignment AlignObj (src),(dst) # Show result DelRes HOH Style Tube
R E F E R E N C E S
[1] Gapped
BLAST and PSI-BLAST: a new
generation of protein database search programs
Altschul SF, Madden TL, Schaeffer AA, Zhang J, Zhang Z, Miller W and
Lipman DJ (1997) Nucleic Acids
Res. 25,3389-3402
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