Hi Friends,
After doing blast for my nucleotide sequence i have found out the homologous sequence based on the identity, sequence coverage and e value. Kindly tell me which tool will be best to find out whether the homologous nucleotide sequences (which i have got by doing blast) are the correct homologous sequences or not?
A typical strategy for verifying a potential ortholog is to use a reciprocal BLAST. Lars describes this in detail in Blast/Reblast to verify homologies so I won't cover it here.
If instead you are trying to get confirmation of the robustness of the BLAST result, then options such as trying alternative search methods (e.g. FASTA and Smith-Waterman), and varying the parameters of the search are possible strategies. Given that you are using protein coding nucleotide sequences, try switch to protein space, so use blastx and equivalents and confirm your nucleotide results against the protein databases. Look at other databases, since you are talking about RefSeq I assume you did your BLAST at NCBI so also have a look at the databases offered elsewhere, e.g. EMBL-EBI, DDBJ, Ensembl, etc.
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What do you mean by 'correct' homologous sequence?
Also be careful with the word "homologous": it has a very specific meaning. Look it up, if you haven't already.
Elena, is this related to your other question where you ask for the position of SNPs in a chromosome if you already know the position in the genes? In that case the BLASTed query sequence should really be transcribed from the chromosome sequence where it is BLASTed against, right?
No Chris this question is totally different from that question.
Ok, so what did you BLAST against what, and what was the purpose?
i did blast against primates and selected few homologous based on their highest sequence identity. to find out exact homologous sequence for my query sequence( NM_000465.2)
Possible duplicate: Blast/Reblast To Verify Homologies
Just wanted to leave these here http://www.sciencedirect.com/science/article/pii/S096800040900005X http://bioinformatics.oxfordjournals.org/content/26/19/2498.full