Fetch Codon Or Amino Acid Alignment Of Certain Genomic Intervals Among 46 Species

Question

[bingyu19821270]

Hello everyone,

In UCSC database, there are genome alignment among 46 verterbrate species. I have hundreds of genomic intervals in human. They are all located in CDS regions. I already fetched the alignment among the 46 species for each genomic interval. The thing is that I also want to know the corresponding codons or amino acids. Can somebody help me out? Thanks a million!

[Vikas Bansal]

Hi. Just for clarification, does it mean you just want to convert your DNA sequence to amino acid sequence?

[bingyu19821270]

Thank you for replying to my question, Vikas. Not exactly. I think I didn't explain it clearly. Say, I have a specific chromosome position in human genome, like, chr3:131102053. It's in CDS region, which is an "A". First, I wanna know whether in other 45 vertebrate species it's also A or other nucleotides. This can be done by using UCSC database, which have alreaday provided the genome alignment of all the 46 species. Second, I wanna know the codon this "A" is in. Let's say if the codon in human is GAG. So I wanna know whether the corresponding codon in other 45 species is also GAG or have changed into other codons, like GTG, GAC..... Thanks anyway.

Answer 1

[Whetting]

Hi,
The easiest approach would be to download the alignments as individual fastA files. At that point it should be easy to translate the nucleotide sequence into three frames. The frame without stop codons would be the correct frame. At that point you can back translate and check the codons. hope this helps

[bingyu19821270]

Hi, Whetting Thank you for your answer. I also thought this might be work, but when I tried, I found that since the alignment contains many gaps in different species and at different positions, no matter which frame I chose, I could always found stop codons in several species.

[bingyu19821270]

Anyhow, Thank you for being willing to help. ^_^