First, as to the differences between CS-Blast and HHpred, please consult the two links below:

http://lmgtfy.com/?q=hhpred+wiki&l=1 http://lmgtfy.com/?q=cs-blast+wiki&l=1

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 >_______________________________________________ >modeller_usage mailing list >modeller_usage@salilab.org >https://salilab.org/mailman/listinfo/modeller_usage

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