Are There Easy Ways To Find Orthologs In Ncbi Nucleartide Database To Do Phylogenetics Analysis?

Question

[Ning-Yi Shao]

Now we have got a sample of bat. We need to decide which species it is in. Based on morphological features, we guess it is a kind of Rhinolophus. I find that in NCBI bank, the known entries are about 1,800. And now I am using 12S rRNA and 16S rRNA to do PCR to build phylogenetic tree, because I found some previous papers used these two mitochondrial rRNA.

My problem is: are there easy ways to find enough orthologs in bank to do phylogenetic analysis?

[Giovanni M Dall'Olio]

why do you need the list of orthologs to identify a specie? You can just blast your sequences directly to genbank, if you have already obtained them.

[Ning-Yi Shao]

Yes, it is a way. But now we only have frozen samples and need to design primer of PCR. Your way is ok if we already have some sequencing result.

[Khader Shameer]

Your question is not clear to me. To check for orthologs you may either need a gene name or sequence. If you are looking for orthologs using a keyword you can search in an ortholog database(COG, eggNOG or Inparanoid). If you have the sequence you could try the BBH based search. I strongly recommend this article for a background reading.

Answer 1

[Dave Lunt]

If you are trying to identify what species it is, I would choose the primers (probably mtDNA) used in some large published phylogenetic or DNA barcoding study of these bats. If you are looking for other loci to PCR you could start with Phylota (http://phylota.net/) which should show you what clusters of sequences are present in Genbank for this genus. It looks like cytochrome b and D-loop are genes with good representation in this genus and Phylota will even let you download an alignment. In order to PCR one of these genes I would find the paper associated with an existing sequence and order the PCR primers the authors used.

[Ning-Yi Shao]

THX! I tried Phylota, yes, it is great. It is feasible and easy to find enriched orthologs in genebank in given taxon.

[Dave Lunt]

I'm not clear what you mean. Can you explain what you want in more detail please. It may be the way you are using "orthologues" that is causing confusion.

[Ning-Yi Shao]

Sorry for my poor expression. Now I want to decide the species of a bat sample. The sample collector said it looks like Rhinolophus affinis based on morphilogical features. There are over 50 species in Rhinolophus, but only about 1,800 sequences in NCBI genebank. I checked some refences about bat, but only few sequences of R. affinis available. Now I want to find a gene that its sequeces are available widely in Rhinolophus, not manully searching. I found Phylota could provide such information now.

[Ning-Yi Shao]

Sorry for my poor expression. Now I want to decide the species of a bat sample. The sample collector said it looks like Rhinolophus affinis based on morphilogical features. There are over 50 species in Rhinolophus, but only about 1,800 sequences in NCBI genebank. I checked some refences about bat, but only few sequences these refences mentioned are available in R. affinis. Now I want to find a gene that its sequeces are available widely in Rhinolophus, not manully searching. I found Phylota could provide such information now.