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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___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org. Please keep all replies on the list by
using "reply all" in your mail client. For discussion of
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