query required by BLASTX

rdu · 01-13-2011, 06:56 PM

From the website, "BLASTX search protein databases using a translated nucleotide query." What does "a translated nucleotide query" really mean here? Shouldn't be a initial genomic DNA sequence, right? A mRNA sequence with "U" replaced by "T"? Would appreciate any help or hint!

kmcarr · 01-14-2011, 06:00 AM

The input (query) which you provide to BLASTX is standard DNA sequence (AGCTN). The BLASTX program then translates this input into protein sequence; the translation is performed for all six possible reading frames. This is what is meant by "translated nucleotide query". The translated sequences are then compared to the protein database you have specified. I don't know off the top of my head how BLASTX deals RNA sequences (AGCUN).

rdu · 01-14-2011, 10:45 AM

Thanks.

Yes, I understand the input should be a standard DNA sequence. The thing confusing me is this DNA sequence should only compose of protein coding parts, or it just a common DNA sequence. That's why I mentioned mRNA sequence with "U" replaced by "T".

Actually, I got a initial genomic DNA sequence data, I try to BLAST it vs. a protein database to have functional analysis, just wondering if i need more steps, or can straightly take BLASTX running.

Mgollery · 01-14-2011, 11:41 AM

No, you don't need any more steps, you can just submit as is to the protein database. Although, if this is a non-coding region, you won't find much.

rdu · 01-14-2011, 12:13 PM

Thanks. Let me take a try.
Have a good day to everyone!

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
blastx against UniProt	papori	Bioinformatics	5	12-26-2012 07:50 PM
blastx parameters for CDS finding	rdu	Bioinformatics	7	12-27-2011 04:21 AM
Blastn or Blastx?	kalu	Bioinformatics	11	09-23-2011 04:18 PM
Help with BLASTX command	z3199001	Bioinformatics	3	10-11-2010 08:51 PM
hardware requirements to run blastX	litali	Bioinformatics	6	09-21-2010 02:55 AM

01-13-2011, 06:56 PM	#1
rdu Member Location: USA Join Date: Aug 2010 Posts: 29	query required by BLASTX From the website, "BLASTX search protein databases using a translated nucleotide query." What does "a translated nucleotide query" really mean here? Shouldn't be a initial genomic DNA sequence, right? A mRNA sequence with "U" replaced by "T"? Would appreciate any help or hint!

01-14-2011, 11:41 AM	#4
Mgollery Junior Member Location: Lake Tahoe, NV Join Date: Jan 2011 Posts: 2	Hello No, you don't need any more steps, you can just submit as is to the protein database. Although, if this is a non-coding region, you won't find much.

01-14-2011, 06:00 AM	#2
kmcarr Senior Member Location: USA, Midwest Join Date: May 2008 Posts: 1,178	The input (query) which you provide to BLASTX is standard DNA sequence (AGCTN). The BLASTX program then translates this input into protein sequence; the translation is performed for all six possible reading frames. This is what is meant by "translated nucleotide query". The translated sequences are then compared to the protein database you have specified. I don't know off the top of my head how BLASTX deals RNA sequences (AGCUN).

01-14-2011, 10:45 AM	#3
rdu Member Location: USA Join Date: Aug 2010 Posts: 29	Thanks. Yes, I understand the input should be a standard DNA sequence. The thing confusing me is this DNA sequence should only compose of protein coding parts, or it just a common DNA sequence. That's why I mentioned mRNA sequence with "U" replaced by "T". Actually, I got a initial genomic DNA sequence data, I try to BLAST it vs. a protein database to have functional analysis, just wondering if i need more steps, or can straightly take BLASTX running.

01-14-2011, 12:13 PM	#5
rdu Member Location: USA Join Date: Aug 2010 Posts: 29	Thanks. Let me take a try. Have a good day to everyone!