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homology search

homology search - Bioinformatics

homology search - Have questions about bioinformatic tools or databases? Post questions here. Discuss and post interesting bioinformatics information.


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Old 07-23-2011, 11:19 AM
Pipette Filler
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Default homology search



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.
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Old 09-27-2011, 01:22 PM
Pipette Filler
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Default Re: homology search

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.
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