[BiO BB] All-again-all protein sequence comparison

Dr. Christoph Gille christoph.gille at charite.de
Fri Dec 17 04:15:53 EST 2004


bl2seq is different to blast since it does list all local matches,
not just one.

There is a web interface that uses the bl2seq output for drawing nice
diagrams. pipmaker I think


> On Thu, 16 Dec 2004, Iddo Friedberg wrote:
>
>
>>
>> Use ncbi toolkit, write a script around bl2seq for the all-vs-all.
>>
>
> Does bl2seq use fastacmd or does it expect two sequences only?
>
>
>
>> If the genomes are really large, I would try and cluster each genome
>> first at 90% Sequence ID, to remove redundancies, using CD-HIT.
>
> Agreed. Run this over a combined database and you already have some
> interesting data. Has anyone played with the new -L coverage cutoff
> threshold in cd-hit?
>
>
>> I wouldn't go with the strategy of having  one genome as a database,
>> and another as a query pool, because that would skew your BLAST
>> statistics to give you false-positive hits. I would go with the
>> all-vs-all pairwise BLAST.
>>
>
> I never used bl2seq, but it might be usefull to run formatdb on the two
> databases anyway, only because it lets you use fastacmd to get any sequence
> (or pair of sequences) out of the database very easily.
>
>
>
>
>>
>> ./I
>>
>>
>>
>> Dr. Christoph Gille wrote:
>>
>>
>>> the ncbi toolkit works well. I can loop over all proteins in one
>>> genome and run blast against the other.
>>>
>>>
>>>
>>>
>>>> Hi, All
>>>>
>>>>
>>>>
>>>> I have been working on obtain the BLAST e-score for all-against-all
>>>>  protein sequences of two genomes. Is there is tool for script for
>>>> this function? Any suggestions will be helpful.
>>>>
>>>> Thanks,
>>>>
>>>>
>>>>
>>>> Anne_______________________________________________
>>>> BiO_Bulletin_Board maillist  -
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>>>>
>>>>
>>>>
>>>>
>>>>
>>>
>>>
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>>
>>
>>
>
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