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How can I search for orthologs ?

I am trying to add new species to molecular phylogeny constructed in previous research. In the previous study, multiple genes from several species were concatenated, aligned and analysed to construct the phylogenetic tree. So, I extracted the genes and got the FASTA file like below. Here I am wondering how I can choose or construct a reference sequence as a query for BLAST in order to retrieve orthologous genes of the new species I want to add.

e.g.) geneA.fasta

>Species A
hogehogehogehogehogehoge...
>Species B
hogehogehogehogehogehoge....
>Species C
hogehogehogehogehogehoge....

There are two options in my mind;

  1. Choose some representative sequences derived from several species in the FASTA file and perform reciprocal best hit with BLAST
  2. Build a probabilistic sequence model of the gene with HMMER and search for the ortholog from the the new species dataset

I am very glad to hear any advice on my trouble. Thank you.

blast hmmer ortholog
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updated by dulankak • dulankak • written by D • D

There exist a large variety of software/tools specifically for this.

Many are alignment based ("BLAST based) but depending on what you want to achieve (or the quality of the result) there exists several approaches.

Perhaps do a google search first ("orthology detection" or such) and see what you get.

Adding new species to an existing analysis will require rerunning much of it from the beginning though. This is because the inclusion of more sequences can (will?) also influence the existing result. Technically it might not be a strict necessity but I would advise to do it anyway, it will only benefit your end result.

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written by lieven.sterck lieven.sterck

Thank you for your advice.

I am going to perform rerunning from alignment with MAFFT, concatenation, and to construction with RAxML-NG or IQ-Tree. My final goal is to perform ancestral state reconstruction with phytools using the new phylogeny.

Anyways, as you say, I will survey the methods or pipelines. Thank you!

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written by D • D

A good point is raised by lieven.sterck

It is tricky to "add" something to an existing phylogeny - it all depends on how robust the result is, and whether the new information fits neatly into the existing tree.

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written by Istvan Albert Istvan Albert

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