Question: Gene Similarity Search
1
gravatar for bow
9.4 years ago by
bow790
Netherlands
bow790 wrote:

I'm looking for a way to search for the most conserved gene in two or more species. For example, if I input 'human' and 'pig', the output would be the top n most conserved gene between humans and pigs (either by nucleic acid or amino acid similarity).

Is there any tool that can do this? At the moment I'm reading UCSC's genome browser documentation to see if this could be done using it, but I'm not sure it could.

conservation similarity • 2.0k views
ADD COMMENTlink written 9.4 years ago by bow790
2
gravatar for Giovanni M Dall'Olio
9.4 years ago by
London, UK
Giovanni M Dall'Olio26k wrote:

The biggest problem is that you have to have a clear definition of 'conserved genes' before proceeding. First, you can align both proteins and dna sequences: so, you have two definition of conservation, whether two genes have similar protein sequence or similar dna sequence. Then, you can also define 'conservation' as having an high rate of synonymous changes compared to non.synonymous ones, and you can include splicing, gene regulation, expression, etc....

One of the approaches you can use is to use a statistics called omega which is the ratio between dN and dS (rates of synonymous/non synonymous changes) between the sequences of two proteins. YOu can go to ensembl/biomart, get the omega value for all genes with their orthologues, and then just sort and get the most conserved values.

ADD COMMENTlink written 9.4 years ago by Giovanni M Dall'Olio26k

I guess for starters, I'll just be looking for the most similar protein sequences. So for example, I would want to know among all the orthologs between humans and zebrafish, which one has the most similar protein sequences.

I've never used biomart before, but thanks for giving me another tool to play with :).

ADD REPLYlink written 9.4 years ago by bow790

note that you can also get % of identity from biomart. Go to biomart, select "Ensembl Genes->Homo sapiens Genes" as dataset, and then in 'Attributes' click on "homologues" and on a species. You can select the values from there. Note that you can't get the omega value directly, you have to calculate dN/dS.

ADD REPLYlink written 9.4 years ago by Giovanni M Dall'Olio26k

Thanks! I tried using filters -> 'orthologous x genes' only and it works, too.

ADD REPLYlink written 9.4 years ago by bow790
1
gravatar for Pierre Lindenbaum
9.4 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum123k wrote:

I guess you can find some interesting data in NCBI/Homologene: ftp://ftp.ncbi.nih.gov/pub/HomoloGene/current/homologene.xml.gz

ADD COMMENTlink written 9.4 years ago by Pierre Lindenbaum123k

Couldn't download the whole thing :/, but I'm browsing the website now. The organism pool is still limited, but it's an ok start. Thanks!

ADD REPLYlink written 9.4 years ago by bow790
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 813 users visited in the last hour