SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
blastx against UniProt papori Bioinformatics 5 12-26-2012 06:50 PM
Using blastn to look for intron/exons boundries alexa039 Bioinformatics 2 01-19-2011 06:05 AM
Using blastn to look for intron/exons boundries alexa039 General 2 01-14-2011 11:45 AM
query required by BLASTX rdu Bioinformatics 4 01-14-2011 11:13 AM
Help with BLASTX command z3199001 Bioinformatics 3 10-11-2010 07:51 PM

Reply
 
Thread Tools
Old 09-03-2011, 07:48 AM   #1
kalu
Junior Member
 
Location: UK

Join Date: Aug 2010
Posts: 6
Default Blastn or Blastx?

Hi everyone,
I have just started annotating a transcriptome of a non-model organism (reads derived from a 454 sequencing) but would like to know what is the best algorithm to do it. I am wondering about blasting the assembled sequences using blastn to identify rRNA genes and genomic DNA and then blast the contigs left using blastx. Does it make sense to you?
Many thanks.
kalu is offline   Reply With Quote
Old 09-04-2011, 12:51 AM   #2
nicedad
Member
 
Location: Switzerland

Join Date: May 2011
Posts: 49
Default

Even though I do not know what do you mean with assembled sequences, almost what
usualy blasted are AllContigs or/and AllIsiotigs. Because these are the results of the assembling process.

cheers,
nicedad is offline   Reply With Quote
Old 09-04-2011, 04:30 AM   #3
kalu
Junior Member
 
Location: UK

Join Date: Aug 2010
Posts: 6
Default

Dear nicedad,

Sorry if I did not make myself clear.. You are right, I meant to blast AllContigs. However my querry is related to which algorithm (blastn or blastx) is the best option to annotate them of a non-model organism.
Many thanks.
kalu is offline   Reply With Quote
Old 09-05-2011, 12:21 AM   #4
Hobbe
Member
 
Location: Uppsala, Sweden

Join Date: Apr 2010
Posts: 29
Default

Did you check out Blast2go.org? I find it to be an excellent and very user friendly option for doing these kinds of annotations.
Hobbe is offline   Reply With Quote
Old 09-05-2011, 04:14 PM   #5
A_Morozov
Member
 
Location: Russia, Irkutsk

Join Date: Feb 2011
Posts: 40
Default

Yeah, that makes sense. Though I think HMMs produce slightly better results when it comes to precisely defining position of RNA gene. For example, try this
http://www.cbs.dtu.dk/services/RNAmmer/
A_Morozov is offline   Reply With Quote
Old 09-06-2011, 05:51 AM   #6
nicedad
Member
 
Location: Switzerland

Join Date: May 2011
Posts: 49
Default

In summary,
BLASTx searchs protein database using a translated nucleotide query whereas blastn for searching translated nucleotide database using a protein query.

best,
nicedad is offline   Reply With Quote
Old 09-06-2011, 11:20 AM   #7
kmcarr
Senior Member
 
Location: USA, Midwest

Join Date: May 2008
Posts: 1,178
Default

Quote:
Originally Posted by nicedad View Post
In summary,
BLASTx searchs protein database using a translated nucleotide query whereas blastn for searching translated nucleotide database using a protein query.

best,
Not quite. blastn searches a nucleotide database with a nucleotide query.

tblastn searches a translated nucleotide database with a protein query.
kmcarr is offline   Reply With Quote
Old 09-07-2011, 01:58 AM   #8
zhidkov.ilia
Member
 
Location: Israel

Join Date: Dec 2010
Posts: 25
Default

The right approach (most probably) will be to use blastx.
(taken from NCBI - tblastx takes a nucleotide query sequence, translates it in all six frames, and compares those translations to the database sequences dynamically translated in all six frames.)
Since you deal with non-model organism, the usage of all six frames in alignment is important.
Although blastx runs for very long time (compared to blastn), the obtained results are much more reliable and worth to wait for.

Ilia
zhidkov.ilia is offline   Reply With Quote
Old 09-23-2011, 11:52 AM   #9
bso
Junior Member
 
Location: Kansas (US)

Join Date: Oct 2009
Posts: 2
Default tBlastx for raw reads?

I am looking for a program that will align translated reads to a related genome (using tBlastx). Optimally, I'd like to visualize this against the translated genome. Maybe I should not try to do this with reads but instead assembled contigs? Any advice?
bso is offline   Reply With Quote
Old 09-23-2011, 12:27 PM   #10
grassgirl
Member
 
Location: Oregon, USA

Join Date: Mar 2011
Posts: 51
Default

What is the advantage of using tblastx instead of blastx in this case? Wouldn't that return a lot of superfluous results since the correct reading frame is the actual protein or am I missing something?
grassgirl is offline   Reply With Quote
Old 09-23-2011, 02:42 PM   #11
bso
Junior Member
 
Location: Kansas (US)

Join Date: Oct 2009
Posts: 2
Default Blastx

Ok yes you're right, blastx-can you recommend a program that will allow me to visualize coordinate (going back to nucleotide) in the genome?
bso is offline   Reply With Quote
Old 09-23-2011, 03:18 PM   #12
grassgirl
Member
 
Location: Oregon, USA

Join Date: Mar 2011
Posts: 51
Default

Hi bso,

I am not sure that I am clear on your objective (my original post regarding blastx was in response to kalu's inquiry...sorry if I didn't make that clear). You have your original read info, so are you asking how to get the nucleotide sequence from the blastx hits (as those will be amino acids)? If so, you can get that info by looking up the GenBank accessions on Entrez, click on the 'Gene' link (or narrow your search by entering Gene in the left dropdown menu) and scroll the the mRNA & protein section lower in the article on that gene, click on the mRNA accession number (should be the left one) and you will see the nucleotide sequence for that hit.

An automated script would be nice for running your hits through.
grassgirl is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 12:03 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO