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Old 08-20-2012, 04:47 AM   #1
Avazeh
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Lightbulb Tool for Human to Gorilla alignment

Hi all,

I have 400 human seqs to align to Gorilla and Chimp. Tried UCSC and got a useful alignment for Chimp but the Gorilla one has supercontigs rather than chromosome numbers

I have to add 2kb to the aligned seqs and then pass to another tool. But his is not possible with just having supercontigs numbers! So I am looking for an alternative.

Any idea or thought would be much appreciated,
Avazeh
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Old 08-20-2012, 07:01 AM   #2
ishmael
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Would you mind to provide more details?
What's the tool you used to do the aignment? liftover?
What's the nature of your data?
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Old 08-20-2012, 07:15 AM   #3
Avazeh
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Sure:

I have 400 human seqs, each between 2kb to 4kb. I need to map them to Gorilla and Chimp and then look for motifs in the extended alignments found. Submitted the regions to UCSC table browser and downloaded conservation in Comparative Genome group, using Multiz Align option to get the sequences in the alignments too. Unfortunately these alignment are just available on gorGOR1 which is the first Gorilla build and contains contig number rather than chromosome number! So I really don't know where on Gorilla genome they hit and cannot extend it to do motif analysis

I need to align my regions to Gorilla's 2011 built, gorGOR3, in which the supercontigs are resolved into chromosomes.

Any help is appreciated
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Old 08-20-2012, 07:27 AM   #4
dpryan
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Quote:
Originally Posted by Avazeh View Post
I need to align my regions to Gorilla's 2011 built, gorGOR3, in which the supercontigs are resolved into chromosomes.
gorGOR3 is available from Ensembl, so I would recommend just downloading the fasta files and aligning to them.
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Old 08-20-2012, 07:28 AM   #5
ishmael
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If all sequences are form human, I would suggest use reciprocal liftover approach.
1. download liftover program from UCSC.
2. download liftover chain files: both of human to gorilla and gorilla to human. You can find them under the genome file download pages.
3. mapping the sequences to human genome, and get the coordination in bed format.
4. convert human bed to gorilla genome by liftover, allow multiple convertion.
5. convert the converted gorilla bed file back to human genome, also multiple loci allowed.
6. filtered the results that the gorilla and human could be converted reciprocally.
That's the protocol I think relatively reliable.
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Old 08-21-2012, 01:47 AM   #6
Avazeh
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Thank you both, will try them out
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