Comparison of sequence homolgy of two genes

Question

[Jimbou]

Hi,

I'm wondering if there is a webtool to compare sequence homolgy of two genes within an organism. So, I want to select two genes, best by gene name like CYP2D6 and compare it's sequence (Exon and/or Intron) against whode genome (like blast) or only one gene like CYP2A6 and get a "homology" score for every exon/intron.

Answer 1

[verma]

Hey Hii,

Please use LALIGN. It may help you to sort your problem.

Regards,
Garima Verma.

[Jimbou]

Thanks.

Answer 2

[h.mon]

I don't think there is an "homology score". Homology is defined in terms of shared ancestry, usually inferred by similarity - for which you can have a score. You may have partial homology, if a gene arose by fusion of two ancestral genes, even so I don't think "homology scores" are used.

Regarding your question, you can use blast to search for paralogs (homologous genes which arose by duplication inside one genome). Indeed, blast has been used many times do to exactly what you want.