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Old 06-06-2013, 05:51 AM   #1
Kawaccino
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Default Blast 2 multifasta files one against the other

Hello everyone,
I have two files: one is a multifasta where each sequence is a contig of interest extracted from an assembled genome.
The second one is also a multifasta where each sequence is a contig of an assembled genome; this file contain the whole assembled genome.
What I want to do is: blast the first file against the second to identify in the second file which contigs are of interest so I can extract them to work only on them and not the whole genome file.
I installed Blast on my computer so I can do it locally and not on the website.
My problem is:
- I tried to perform a blast2seq, and nothing, it doesn't work, in fact, it just blast the first sequence of the file 1 against the first sequence of the file 2. And then it stops
- so I tried to transform my whole genome fasta file in a database (with formatdb -i file.fasta -p F) and I did a blastn but it didn't work either.

So my question is: how can you blast two multifasta files one against the other?

Thank you very much for any help you can provide me.
Cordially,
K.
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Old 06-06-2013, 09:22 AM   #2
rhinoceros
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Quote:
Originally Posted by Kawaccino View Post
So my question is: how can you blast two multifasta files one against the other?
You could define the other file as a subject and the other as a query. However, it'll be much faster if you create a db from the other file (i.e. you can run a multithreaded blast). I have no idea why your attempt failed. Perhaps if you told us what was it exactly that you did, and what the actual error message was. Also, consider reading the blast manual?


p.s. A question to all. Why is legacy blast usage still so common?
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Old 06-06-2013, 09:38 AM   #3
GenoMax
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Blat would likely work well for this as well. No need to mess with creating databases etc. You can produce output in a blast like format if you want to visually check the alignments.

http://genome.ucsc.edu/FAQ/FAQblat.html

Last edited by GenoMax; 06-06-2013 at 09:43 AM.
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Old 06-06-2013, 09:42 AM   #4
GenoMax
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Quote:
Originally Posted by rhinoceros View Post

p.s. A question to all. Why is legacy blast usage still so common?
Perhaps because some of us are old enough to have started practicing "bioinformatics" (it was not called that back then) with blast

On a serious note:

There is a good bit of history/theory available for blast.
Statistics are well documented and understood.
Easy web based interface to do searches.

I am sure others will add to this list ..
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Old 06-06-2013, 11:10 AM   #5
Kawaccino
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Hey!
Thank you all for the help, I think I will see Blat.
Concerning Blast I read the manual and it says nothing that helped me with my problem. By the way I don't get any Error message; the job finishes and when I open the output file, there is nothing in it.
I aligned the two files with Mauve, and there are alignments between the two files, so I should obtain something with Blast...
Thanks again,
K.
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Old 06-06-2013, 10:56 PM   #6
rhinoceros
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Quote:
Originally Posted by Kawaccino View Post
Hey!
By the way I don't get any Error message; the job finishes and when I open the output file, there is nothing in it.
How long does the job run? Try to search just one sequence against your db to see if it works at all. Are you sure your files are in proper fasta format - only headers and sequences and nothing else?

p.s. If you're having problems on setting up blasts properly, I'd not recommend blat for the time being..

Last edited by rhinoceros; 06-07-2013 at 01:24 AM.
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