Question: Tools For Validating Blast Result?
1
gravatar for Elena
9.6 years ago by
Elena240
Elena240 wrote:

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?

blast genomics • 1.8k views
ADD COMMENTlink written 9.6 years ago by Elena240
10

What do you mean by 'correct' homologous sequence?

ADD REPLYlink written 9.6 years ago by Farhat2.9k
6

Also be careful with the word "homologous": it has a very specific meaning. Look it up, if you haven't already.

ADD REPLYlink written 9.6 years ago by Neilfws49k

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?

ADD REPLYlink written 9.6 years ago by Chris Evelo10k

No Chris this question is totally different from that question.

ADD REPLYlink written 9.6 years ago by Elena240

Ok, so what did you BLAST against what, and what was the purpose?

ADD REPLYlink written 9.6 years ago by Chris Evelo10k

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)

ADD REPLYlink written 9.6 years ago by Elena240

Possible duplicate: Blast/Reblast To Verify Homologies

ADD REPLYlink modified 13 months ago by RamRS30k • written 9.6 years ago by Michael Schubert7.0k
2
gravatar for Hamish
8.7 years ago by
Hamish3.1k
UK
Hamish3.1k wrote:

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.

ADD COMMENTlink modified 13 months ago by RamRS30k • written 8.7 years ago by Hamish3.1k
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