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-   -   tblastn and blastx question (http://seqanswers.com/forums/showthread.php?t=46808)

Nepa10 09-21-2014 05:05 PM

tblastn and blastx question
 
It says that tblastn is more likely to find distantly related sequences than the blast, blasts, and blastp. I wonder why is it? I generally use Blastx.

By definition, tblastn compares query protein sequence with the database after translating each nucleotide sequence into protein using all six reading frames

whereas

Blastx first translates query sequence into amino acids in six reading frames (three forward and three back) then compares the protein sequences with protein databases.

Any insight would be greatly appreciated!

Thanks.

reema 09-22-2014 07:10 AM

But in order to find distant related sequences I used Psi-blast. Here the link http://www.protocol-online.org/biolo...sts/26387.html

Nepa10 09-23-2014 07:12 PM

Hi, thank you very much. I realized that Psi-blast is an option available through blastp. Seems like Psi-blast is more rigorous that blastX.

I am little bit confused about the difference between blastp and blastx. They both blast against protein databases but the difference is in query sequences, for example protein sequences for blastp. However, in blastx, query sequences are translated nucleotide sequences, which are also protein sequences. So how are these two methods different?

Thanks!

reema 09-24-2014 12:07 AM

Please see https://blast.ncbi.nlm.nih.gov/BLAST_guide.pdf. Especially page number 9 and question 4.9.
I hope this helps.

Thanks,
Reema


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