[BiO BB] Is there a good way to find orthologue sequences?

[Marcos Oliveira de Carvalho]

Another good discussion about orthology and paralogy can be found here:

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=retrieve&db=pubmed&list_uids=12446146&dopt=Abstract

And Lerat et al, presents a novel approach for determining orthology in:

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12975657&query_hl=4

Marcos




On Fri, 17 Jun 2005 17:04:01 -0300, Diego Martinez <sariego9 at yahoo.com>  
wrote:

> commonly the only way one will use the term
> orthologous is if you are using all the genes
> of 2 genomes.  The reasoning goes like this:
> for gene A in genome 1, and for gene B in
> genome 2, if the highest scoring hit to gene A
> from genome B is gene 2, and if the highest
> scoring hit to gene 2 from genome A is gene
> 1, then gene 1 and gene 2 are potential
> orthologs.  I hope I said that right.
> This is called either bi-directional
> best hits or mutual best hits.  It might
> be easier to draw out also.
> Most researchers I know who deal with
> this sort of thing conclude that without the
> entire genome, you can not really
> be sure that you are looking at a true
> ortholog, it could be a "co-ortholog"
> or as Christoph said, a paralog.
> Also see Overbeek et al (PNAS v.96(6); Mar 16, 1999)
>
> Diego
>
> --- "Dr. Christoph Gille" <christoph.gille at charite.de> wrote:
>
>> There is always the danger of picking a paralogous sequence instead.
>> If two genes are orthologous then the sequence identity should be
>> typical for the two species.
>> If they are paralogous the sequence identiy is higher.
>> I am not convinced that this can be solved completely automatically.
>>
>> Christoph
>>
>>
>>
>>
>> > Dear all,
>> > Is there a good way to find orthologue sequences? I mean, I have a
>> > protein sequence in species A, how could I get all the available
>> > corresponding sequences from other species?  I blast my sequence to  
>> nr,
>> > there are just too many hits with low e-value and high identity, so  
>> that
>> > some "corresponding" sequences from distant related species could not  
>> be
>> > find by blast. Is there any good method for automatically solve this
>> > problem?
>> >
>> > Thank you very much.
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