homology search

[ishabioinfo]

Hello everyone,

Which program is most accurate and fast for homology sequence search for conserved hypothetical protein sequences. Actualy i want to know which program will be best for this job among BLASTP, PSI-BLAST, PHMMER or JACKHMMER?


Kindly do reply of this question soon

Thanx all.

[verginov - metalife.com]

It depends of what you need to compare. If you want to do a comparison of a single sequence against a sequence database in order to find if it shares conserved region (domain) with another sequences you have to use PSI-BLAST. The algorithm will include your sequence (or part of it) in a position-specific scoring matrix and will continue searching the database for new matches with the generated PSSM. If you want to find out a specific domain in your sequence, then use PHHMER - the algorithm will compare your FASTA sequence to a HMMPfam database which is an excellent collection of precalculated Hidden Markov Models of well annotated functional domains.