There is no absolute way to answer your second question. CS-BLAST provides
only a starting (and context-dependent) checkpoint for BLAST or PSI-BLAST,
from which those programs usually find more homologues than when they start
from a single protein sequence. HHpred, however, further uses all sequences
found by PSI-BLAST, aligns them and makes hidden Markov models, and then
performs HMM-HMM search which is at present the most sensitive way to
detect homology. The problem with HHpred is that even though it is most
sensitive, it doesn't contain all PDBs in its library, so PSI-BLAST
jump-started by CS-BLAST may still end up finding a better alignment simply
because, unlike HHpred, it searches against all PDB sequences out there.
Publications about both methods and their respective web pages offer clear
descriptions of what each approach can do. Shouldn't be too hard to find
them using PubMed.
Take care,
Mensur
At 03:37 AM 12/19/2011, you wrote:
Respected Sir,
First of all sorry for a bit unrelated question to MODELLER, but please
tell me, what is the difference between
1. CS-BLAST
2. HHpred
Who is the best of these two at searching most reliable homologoua
templates (PDBs) for a target sequence? I am not able to find differences
between these two.
Thank you Sir and Sincerely,
Ashish
Ashish Runthala,
Lecturer, Structural Biology Cell,
Biological Sciences Group,
BITS, Pilani
Rajasthan, INDIA
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