Features Download
From: Dan kilburn <dr_kilburn59 <at> yahoo.com>
Subject: Re: Bioperl-l Digest, Vol 117, Issue 13
Newsgroups: gmane.comp.lang.perl.bio.general
Date: Wednesday 30th January 2013 21:40:26 UTC (over 3 years ago)
Hi Jason,

Are there any plans to keep SearchIO up to date with ncbi blast? I know
they change formats ridiculously often, but I had to write my own parser to
get sequence identity, which I would rather not have done. I realize that
this job would be a big load on anyone who takes it, but it's so
fundamental. Maybe I can help.

Sent from my iPhone

On Jan 30, 2013, at 12:00 PM, [email protected] wrote:

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>   1. Re:  Parsing Blast-Report extracting "Features flanking    .."
>      (Jason Stajich)
> ----------------------------------------------------------------------
> Message: 1
> Date: Tue, 29 Jan 2013 11:00:16 -0800
> From: Jason Stajich <[email protected]>
> Subject: Re: [Bioperl-l] Parsing Blast-Report extracting "Features
>    flanking    .."
> To: [email protected]
> Cc: [email protected]
> Message-ID: <[email protected]>
> Content-Type: text/plain;    charset=us-ascii
> We don't parse the NCBI feature info from the BLAST reports per your
query. To look up a specific feature you can use Bio::DB::GenBank to query
for sequence from a specific feature by accession number - see the HOWTOs
for that.
> However, most people use tools that generate SAM/BAM files with short
reads - then you can use a tool like bedtools to find overlaps of reads
with the locations of features.
> basically:
> - download the genome and GFF for arabidopsis
> - align your sRNA to the genome with a short read aligner - bowtie, bwa,
> - convert your sam to bam file with SAMtools or picard
> - compare the location of features with the reads to get expression
summaries or individuals reads with BEDTools
> On Jan 25, 2013, at 2:20 AM, jobu  wrote:
>> Am 22.01.2013 19:03, schrieb Mgavi Brathwaite:
>>> What upstream and downstream elements are you interested in?
>> I've got a huge pile of short RNA reads.
>> Part of the question now is whether those RNA fragments originate from
>> siRNA events,
>> or may represent miRNAs / parts of pre-miRNAs.
>> So I did an online  blast search against database nt.
>> The resulting report quite often just gives subject information like
>> -----
>>> gb|CP002686.1| Arabidopsis thaliana chromosome 3, complete sequence
>> Length=23459830
>> -----
>> Now I would like to get the hit's neighbouring regions  for further
>> analysis.
>> Preferably I would like to do that  in an automized way, but the only
>> possible action with this kind of subject gi | description would be to
>> fetch the entire chromosomal  sequence I guess ?
>> However,
>> right below the line above, the report states more precisely:
>> ------
>> Features flanking this part of subject sequence:
>>  8872 bp at 5' side: cytochrome P450 90B1
>>  402 bp at 3' side: U1 small nuclear ribonucleoprotein-70K
>> ------
>> Still I would like to have the possibility to automatically fetch the
>> subject's sequence(s),
>> as of now I think  parsing the report with SearchIO won't let me aquire
>> that information, because SearchIO does not recognize report sections
>> like those.
>> I hope I did not miss any of SearchIOs capabilities, but I could not
>> find any method covering my wish?!
>> Right now maybe the only way to get the information I want is to
>> construct my own parser and write it out into a separate file, which in
>> turn again  I could read into a hash before processing the Blast-Report
>> with SearchIO to combine both data for further automized work.
>> I am aware though that even successfully getting the flanking features
>> would leave me with the more or less wide  intergenic gap my hsp is
>> located in.
>> However I'm in need of a way to get the flanking features including
>> their annotation and the region spanning between them.
>> But I hope I do not have to get complete sequences to accomplish that,
>> as this would be kind of an overkill.
>> with kind regards
>> Jochen
>> _______________________________________________
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> Jason Stajich
> [email protected]
> [email protected]
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> End of Bioperl-l Digest, Vol 117, Issue 13
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