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

[Brian Osborne]

Michael,

Jonathan King! That's funny. An unconventional thinker who was way ahead of
his time in some ways, he had this notion of a protein folding imtermediate
many years before it was accepted, and he studied these intermediates as a
phage geneticist, not as a crystallographer or structural biologist.

Brian O.


On 6/21/05 8:52 AM, "michael watson (IAH-C)" <michael.watson at bbsrc.ac.uk>
wrote:

> 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+Searc
> h&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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>> 
>> 
>> 
>> 
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> 
> 
> 
> 
>