Hi Patricia,

If your data is still in MAF format, first convert it to FASTA using the tool "Convert Formats -> MAF to FASTA". Next, translate the regions using the tool "EMBOSS -> transeq".


Depending on where your intervals are located, the data may get confusing at the translation step if you are not sure of the starting human frame or if it is mixed, but there isn't really another good solution from this point. If this is a problem, you could always back up and start with intervals having a known frame for all (for example, +1 for human) or group the intervals by common human frame before extracting the MAFs. If you used the tool "Stitch Gene blocks", then you should not have any problems (it is designed to preserve reference frame +1 for the merged coding exon intervals when the default options are used).

The FASTA translations for a "gene" or group of related "intervals" can be sent to the tool "Multiple Alignments -> ClustalW" to view the resulting translations back in a stacked alignment format. The tool "Motif Tools -> Sequence Logo" may also be of interest for viewing/graphing results.

More about the MAF tools available in Galaxy:
Making whole genome multiple alignments usable for biologists
http://www.ncbi.nlm.nih.gov/pubmed/21775304
http://main.g2.bx.psu.edu/u/dan/p/maf

Hopefully this helps,

Jen
Galaxy team

On 7/11/12 1:04 AM, bingyu19821270 wrote:
Hi all,
I am a new Galaxy user and I have searched the mail list, looking for the 
answers to my questions, but failed.
I am trying to fetch the corresponding codon or amino acid alignments among 46 
species using genomic intervals in human.
I know if I have a list of human genomic intervals, I can get the nucleotide 
alignments of these intervals among 46 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!
--------------------------------------------------------------------------------
Patricia Hsu
Kunming Institute of botany, CAS
------------------------------------------------------------------------
bingyu19821270


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