The best way to obtain chimp regions orthologous to your human intervals is to fetch
human-chimp alignments and convert the same to intervals. Here's how this can be
1. Use "Fetch alignments > Extract pairwise MAF blocks" tool to extract
human-chimp alignments corresponding to your human intervals. Before using this tool,
please make sure that your input file is of interval/bed format and the build is set to
human (hg18/hg19). You can click the pencil icon next to your dataset name to modify these
fields if necessary.
2. Use "Convert formats > MAF to Interval" tool (and select chimp under
additional species) to convert the output of step 1 to intervals. This tool will return
two files - one with human intervals that could be aligned with chimp and the other with
Hope this answers your question.
Thanks for using Galaxy,
On Apr 30, 2010, at 5:17 AM, research pal wrote:
From: research pal <workinformatics(a)yahoo.com>
I have a bed file for the chimp genome and I want to download the same region for
the human genome.
Do you have a tool in Galaxy which can help me for these orthologus regions.
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