obstain 100-way alignment of 100 species for a certain gene

Question

[qwzhang0601]

I want to get the alignment file (Amino acid for protein, and nucleotide for CDS) for a particular gene from 100-way alignment of 100 species (http://hgdownload.cse.ucsc.edu/goldenPath/hg19/multiz100way). Is there an easy way to get it?

Thanks

[microfuge]

If your focus is a single gene (largely CDS) then it would be good to take a look at ensemble compara For example (https://www.ensembl.org/Homo_sapiens/Gene/Compara_Ortholog?db=core;g=ENSG00000139618;r=13:32315086-32400266) . You can download alignment of 100 plus species for one to one orthologs ) The UCSC alignments typically are genome alignments.

[qwzhang0601]

Thank you for your suggestion. I tried to get the alignment, but it seem it generate the alignment on the gene DNA sequence level (including noncoding part), right? I see many long gaps in the alignment. Is there a way to only include CDS sequence or protein sequence? Thanks

Answer 1

[GenoMax]

You can find those alignments here. You will need to download the entire set and then find the gene/exons you need in that file.

It may also be worth looking at NCBI's homologene project where you would be able to search for one specific gene.

[qwzhang0601]

Thanks. I got the files (like refGene.exonAA.fa.gz) from the link you provided. But it seems, it only includes alignment on exon level. We need to merge all exons by myself. Am I right? Not sure whether there is a direct way to do this, or any tool can help to merge alignment of exons into alignment of a gene.

I also looked at NCBI homologenes, but only found alignment for 10 species.

Thank you again for your suggestions.