[BioC] BLAST search sequence for species ID from R?

[jos matejus]

Dear all,

Many thanks for all the advice, it is greatly appreciated. I am always
impressed by the amount of time and effort people are willing to give.
I'll let the list know how I get on.

Seasons greetings to you all
Jos

On Monday, December 14, 2009, Sean Davis <seandavi at gmail.com> wrote:
> On Mon, Dec 14, 2009 at 6:02 AM, jos matejus <matejus106 at googlemail.com> wrote:
>> Dear list members,
>>
>> A colleague has asked whether I can help him with a bioinformatics
>> problem he has as he knows I use R (although I don't usually use R for
>> this type of problem) and I was hoping someone might be able to point
>> me in the right direction. I have searched the mailing list archives
>> and also Googled this particular query, but without success. I ask
>> forgiveness in advance if the question is not appropriate for this
>> forum.
>>
>> Anyway, the background is that my colleague has a sample collected
>> from the field containing many species of related insects (same genus)
>> which he has obtained lots of sequence information (from 454). The
>> sequences are saved in a single fasta file. What he wants to do is to
>> query Genbank to match each sequence from the fasta file to particular
>> species (A nucleotide blast search I believe) and return the top
>> ranked match for each sequence. He can do this manually via the web
>> page, but he will have a lot of these files in the future and was
>> looking for some way of automating the process (hence using R). He
>> ultimately wants to be able to restrict the Blast search to a list of
>> preselected  Accession numbers or within genus.
>>
>> As I am not familiar with this field I was wondering whether anyone
>> knows of an existing function (or functions) that can do the job. I am
>> looking at the package seqinr at the moment to see whether this would
>> fit the bill and also whether the Biostrings package would be
>> appropriate. However, the learning curve looks a little steep and I
>> wanted to make sure I was going down the right road before investing
>> lots of time.
>>
>> Also, is there a package that I can use to access the Genbank database
>> directly from within R to do the Blast searches?
>
> Hi, Jos.
>
> R/Bioconductor has the tools that you could use to rewrite blast if
> you like, but for cross-species comparisons, blast is a pretty good
> tool.  You might consider downloading the blast source or a convenient
> binary from NCBI and running it locally.  Of course, a command-line
> utility like blast can be easily scripted from R.  As for getting
> records from GenBank, consider whether you need programmatic control
> over the process at all.  It may be that your colleague already has a
> way to get the sequences he/she wants directly and just wants help
> with running blast.  However, if it does appear that programmatic
> access is necessary, have a look at the EUtilities web services.  With
> EUtilities, it is pretty straightforward to construct a URL, use
> something like getURL() from the Rcurl package, and get the results.
>
> Hope that helps.
>
> Sean
>