[Chimera-users] On the seeking of the orthologs

[James Starlight]

Elaine, George, thank you very much for the suggestions and ideas!!

One question- do you know some DB where is possible to seek for the
orthologs (e,g based on HMM) agains *several* target sequences with
flexible options like to detect minimal percent of the homology for
orthologs which to be found or alternatively to make such search based
on some *shared* features between those targets (e.g common structural
motifs responsible for ligand binding etc) which might be specified by
user initially?

George, the idea to focus on particular specie seems interesting-
initially I've thought in the same way but to focus on the human OR
(because here I'm more comfortable with dynamical range patterns of
those receptors based on the in vivo Matsunami data for instance). BTW
briefly have a look on those DB I didn't find there engine to seek for
the orthologs agains given target. Doest this option really exist
within it?

All the best,

James

2015-05-22 21:10 GMT+02:00 George Tzotzos <gtzotzos at me.com>:
> I would start from BioMart. I’m also working on OR (albeit insect ones). Try also MGI (Mouse Genome Informatics). Starting from mouse Ors you can scoop orthologs in other mammalian species.
>
> Cheers
>
> George
>
>> On 22 May 2015, at 18:44, Elaine Meng <meng at cgl.ucsf.edu> wrote:
>>
>> Hi James,
>> Your questions are more about bioinformatics project design rather than Chimera use.
>>
>> Chimera provides basic BLAST searching of NCBI’s “nr” and “pdb” sequence databases, but these are the same databases generally used by BLAST whether you use it from Chimera or from another program, or stand-alone.  Also, Chimera can fetch specific individual sequences from UniProt based on UniProt identifier, but that isn’t searching, it is just getting data you already knew you wanted.
>>
>> I believe NCBI’s “nr” and UniProtKB are both meant to be comprehensive (cover “all” sequences) but in their own ways, and you would have to go to those resources or their publications to learn the details.  There are probably also specialized GPCR and/or olfactory receptor sequence databases.  Then there are multiple ways of searching, with individual sequences or with derived patterns  such as hidden Markov Models (HMMs).  This is a really broad topic and in my opinion, beyond the scope of this forum.  You’ve probably done some of this already, but I would recommend reading similar studies in quality journals by authors you respect, to see how they have designed their projects.
>>
>> Chimera doesn’t have HMM-related tools or evolutionary trace, it just allows conservation analysis on your whole alignment, or subsets of that alignment opened in separate windows.
>>
>> I hope this helps,
>> Elaine
>> -----
>> Elaine C. Meng, Ph.D.
>> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
>> Department of Pharmaceutical Chemistry
>> University of California, San Francisco
>>
>> On May 22, 2015, at 9:22 AM, James Starlight <jmsstarlight at gmail.com> wrote:
>>
>>> Dear Chimera users!
>>>
>>> I'd like to ask some suggestion regarding my bioinformatician task and
>>> possible ways of its realisation using some bioinformatics methods
>>> implemented in Chimera.
>>>
>>> 1)I need to seek for some sequence database (here I don't know
>>> absolutely how to do it) of the olfactory receptors and to select 10
>>> sequences of the Ors corresponded to 10 different mammalian species ->
>>> according to my idea it should be very different species associated
>>> with different ecological niches so its olfactory spectrum should vary
>>> dramatically.
>>> Here the question: in what DB such search should be better with the
>>> inclusion of flexible search criteria's like what I've listened above?
>>>
>>> 2)After allocating of those 10 sequences I should to find *all*
>>> possible orthologs against them-> to find all OR in another species
>>> which have conservation degree agains target above chosen threshold .
>>> Eventually I'll need to make some analysis regarding overall
>>> conservation of the OR within different species and to point out what
>>> OR are most important (conservative) in different organisms in
>>> accordance to some pre-defined criteria's (i.e ecological niche of the
>>> species because it's associated with the odor spectrum). Here the
>>> question: would the methods like blast-search be enough for such task
>>> or I should to use also methods like evolutional tracing (to find all
>>> important residues in different OR which tend to co-evaluate) based on
>>> its alignment data?
>>>
>>> I would be very thankful for any suggestion!
>>>
>>> James
>>
>>
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