Whole genome alignment of Chimp on hg19 in FASTA format

[Guillaume Dumas]

Dear UCSC Staff,

I am trying to recover a FASTA file of the Chimp genome aligned on hg19, in a similar fashion of the 6epo ancestor sequence.

On the UCSC website, I found AXT alignment files but I can't find a straightforward solution to convert them into one whole genome FASTA.

Do you know if there is already such FASTA to download somewhere or a tool that may help converting those AXT alignment files?

Best regards,

Guillaume

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Guillaume Dumas, M.Eng., M.Sc., Ph.D.

Research Fellow | Human Genetics and Cognitive Functions Lab. | Institut Pasteur

Associate Member | Center for Complex Systems and Brain Sciences | F.A.U.

Co-Founder | HackYourPhD.org | "Science and Knowledge as a common goods!"

[Steve Heitner]

Hello, Guillaume.

Are you just looking for one whole FASTA file of the chimp genome in general?  You can do this by downloading the panTro4.2bit file from http://hgdownload.cse.ucsc.edu/goldenPath/panTro4/bigZips/ and using the twoBitToFa utility to convert it to FASTA format.  You can obtain the twoBitToFa utility from http://hgdownload.cse.ucsc.edu/admin/exe/.

Please contact us again at gen...@soe.ucsc.edu if you have any further questions.  Questions sent to that address will be archived in a publicly-accessible forum for the benefit of other users.  If your question contains sensitive data, you may send it instead to genom...@soe.ucsc.edu.

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Steve Heitner
UCSC Genome Bioinformatics Group

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[Guillaume Dumas]

Hello Steve,

thanks for your answer. I am looking indeed to the whole Chimp genome in FASTA, but aligned to hg19, as in the Chimp table of the UCSC Browser:

​

Any idea of how I can dowload this track?

Best regards,

Guillaume

[Steve Heitner]

Hello, Guillaume.

I believe you may be interested in MAF format (http://genome.ucsc.edu/FAQ/FAQformat.html#format5).  We have a axtToMaf utility available for download at http://hgdownload.cse.ucsc.edu/admin/exe/.

You may also be interested in the following utility available at Galaxy: https://toolshed.g2.bx.psu.edu/repository/display_tool?repository_id=ecc93bc8f0382e9e&tool_config=tools%2Ffilters%2Faxt_to_fasta.xml&changeset_revision=c2a356708570.  You should contact Galaxy for support with any Galaxy tools (https://wiki.galaxyproject.org/Support).

Questions sent to that address will be archived in a publicly-accessible forum for the benefit of other users.  If your question contains sensitive data, you may send it instead to genom...@soe.ucsc.edu.