[BiO BB] orthologs vs in-paralogs

[Dan Bolser]

> This is a good question, please drop me a note if you guys get some answers.
>
> For all I know, besides the homolog part, the key difference is that ortholog  is
> same function in different species, while paralog is different function in  same
> species.

Yup, I know this definition, but it doesn't address the idea or redundancy within a
genome. This is (apparently) a big issue for functional genomics.

Cheers


> Please keep me posted!
> Thanks!
> haibo
> //cheers
>
> Quoting Dan Bolser <dmb at mrc-dunn.cam.ac.uk>:
>
>> Phil Luo said:
>> > Dear all,
>> >
>> > As we know ,there are two kinds of homolog, ortholog and paralog.
>> Genes in two
>> > species that have directly evolved from a single gene in the last
>> common ancestor
>> > are called orthologs. A set of homologous genes that have diverged
>> from each other
>> > as a consequence of genetic duplication are called paralogs. Sometime
>> those
>> > paralogs which arose from a duplication after the speciation event are
>> called
>> > in-paralogs.
>> >
>> > My question is how to distinguish the in-paralogs from orthologs.
>> Which one is
>> > supposed to be more similar, in-paralogs or orthologs?
>>
>> Hi,
>> Good question! Maby someone on the sequence searching mailing list can help
>> answer,
>>
>> http://bioinformatics.org/mailman/listinfo/ssml-general
>>
>>
>> I know of some work trying to uncover 'lineage specific gene expansion' by
>> Eugene
>> Koonin (sp?) at the NCBI. That sounds a bit like the in-paralogues you describe.
>> Also he and coworkers define an algorithm for predicting orthologous pairs,
>> simply
>> 'best hits' between genome 1 and 2.
>>
>> Although I understand the definition of orthology and paralogy, I find the
>> concepts
>> a bit confusing. I don't know what information you loose by simply talking about
>> gene families, and ignoring the within / between genome distinction.
>>
>> At some level does't ortholog mean 'same gene', and paralog mean 'copy'?
>>
>> Cheers,
>>
>> > Best regards,
>> > Phil
>> >
>> >
>> > ---------------------------------
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>>
>>
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>
>
>
> =========================================================
> Haibo Zhang, PhD student
> Computational Biology, NJIT & Rutgers University
> Center for Applied Genomics, PHRI
> http://afs13.njit.edu/~hz5