Multiple Sequence Alignment Of Unigenes From Several Different Species

Question

[jianfeng.mao]

I have unigenes from several different species (in fasta, from transcriptome NGS sequencing, without whole genome reference seq for any species), I would like to implement evolutionary analysis by comparing those homologous genes among the species. The whole study could be divided as several steps:

1. the infer the orthologous genes by multiple sequence alignment of all those unigenes from different species.
2. infer the coding region for each such genes identified as orthologs
3. apply evolutionary calculation on those aligned coding sequences

I will very appreciate those who can share with me advice/directions on tools/strategies to generate such a multiple sequence alignment. I am now aware of some potential tools, blast, megablast, DIALIGN-TX (http://dialign-tx.gobics.de/), while I have no experience. How do you compare different tools? Do you have any further recommendations?

Thanks in advance.

Looking forward to hearing from you.

Answer 1

[Rahul Sharma]

Hi,

I would use OrthoMCL or Inparanoid/multiparanoid for orthologs prediction. For multiple sequence alignments I would use MAFFT or MUSCLE aligner. This would depend on your analysis, if you are thinking to perform the positive selection studies on these orthologs gene, I would use prank-codon multiple sequence aligner.

Wishes, Rahul