Among the multiple entries of sequences for same protein of a specific organism in any database, which entry should be used for further task? Is there is any specific criteria to select such protein sequence? It it better to use refseq records?
In general when we search any protein of a specific organism in Entrez, we often get multiple entries. The sequence does not have too much differences but in mutation based studies these differences can be crucial. So, what should be criteria of selecting one sequence among multiple sequences.
A good starting point is to use the reference sequence for that species as that is likely to be used by a wider group of people for comparative studies. Many organisms have had their genomes sequenced and the annotations submitted to the public archival databases (INSDC). Check out UniProt's complete proteome page:
http://www.uniprot.org/taxonomy/complete-proteomes
I agree with the recommendation of using RefSeq. However, your own sequence may be different. I've seen minor differences between my own and the database sequence for proteins I've worked on. You might want to try to clone or PCR your own gene and determine the sequence yourself.
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