[Bioperl-l] how to get entries from swiss-prot

[michael watson (IAH-C)]

Actually, the phrase "phage organelle", when enclosed in speech marks, is almost a googlewhack ;-)

http://www.google.co.uk/search?hl=en&q=%22phage+organelle%22&btnG=Google+Search&meta=

However, there is one paper that refers to a phage tail as an organelle:

http://jb.asm.org/cgi/content/full/185/14/4022


-----Original Message-----
From:	Brian Osborne [mailto:brian_osborne at cognia.com]
Sent:	Tue 21/06/2005 1:41 PM
To:	michael watson (IAH-C); Baoqiang Cao; bioperl-l at portal.open-bio.org
Cc:	
Subject:	Re: [Bioperl-l] how to get entries from swiss-prot
B.,

You mean "phage" or "organelle", yes? Phages, or bacteriophages, do not have
organelles so combining these 2 terms with AND is going to retrieve very few
entries.

As Michael suggested, you could try Bio::DB::Query, it's described in the
Beginner's HOWTO:

http://bioperl.org/HOWTOs


Brian O.


On 6/21/05 5:56 AM, "michael watson (IAH-C)" <michael.watson at bbsrc.ac.uk>
wrote:

> I just did an SRS all text search of swissprot at the EBI:
> 
> Query "(([swissprot-AllText:phage*] & [swissprot-AllText:organelle*]) |
> [swissprot-AllText:phage organelle*]) " found 1 entries
> 
> Even searching the whole of uniprot only throws up two entries.
> 
> So either SRS isn't working as expected, or you don't really have much of a
> problem here....
> 
> Failing that, you can use the Bio::DB::Query interface to search the protein
> database at the NCBI - doing a quick search, entrez throws out 9 results for
> phage organelle :-)
> 
> -----Original Message-----
> From: bioperl-l-bounces at portal.open-bio.org on behalf of Baoqiang Cao
> Sent: Mon 20/06/2005 8:53 PM
> To: bioperl-l at portal.open-bio.org
> Cc: 
> Subject: [Bioperl-l] how to get entries from swiss-prot
> Dear All,
> 
> I'd like to download all entries in swiss-prot with keywords "phage
> organelle", any package I can use for this purpose? Thanks.
> 
> Best,
>  B. Cao
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