tblastn and blastx question

Nepa10 · 09-21-2014, 06:05 PM

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, 08:10 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, 08:12 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, 01:07 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

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
Blastx similarity %	jevcampe	RNA Sequencing	1	03-18-2015 05:21 AM
Blastx	Desai	Bioinformatics	1	01-27-2014 11:50 PM
Inquiry of Parsing tblastn result to get nucleotide sequence from the db file	sunfuhui	Bioinformatics	2	09-12-2012 06:39 AM
Learn how to use Blastx	angeloulivieri	Bioinformatics	4	07-09-2012 01:25 AM
Help with BLASTX command	z3199001	Bioinformatics	3	10-11-2010 08:51 PM

09-21-2014, 06:05 PM	#1
Nepa10 Junior Member Location: US Join Date: Jun 2014 Posts: 8	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.

09-22-2014, 08:10 AM	#2
reema Member Location: Scotland Join Date: Feb 2014 Posts: 27	But in order to find distant related sequences I used Psi-blast. Here the link http://www.protocol-online.org/biolo...sts/26387.html

09-23-2014, 08:12 PM	#3
Nepa10 Junior Member Location: US Join Date: Jun 2014 Posts: 8	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!

09-24-2014, 01:07 AM	#4
reema Member Location: Scotland Join Date: Feb 2014 Posts: 27	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