[Genome] Restriction enzyme track not on table browser?

[Aaron Tenney]

I'd like to download the information on the restriction enzyme track
in the mapping and sequencing group but it doesn't appear in the
table browser. Is there any way do download this track?

Aaron

[Rachel Harte]

Aaron,
You can obtain some information about the Restriction Enzymes through the
Table Browser. If you select All Tables on the group pulldown menu, then you
can select hgFixed for the database. The table for restriction enzyme data is
called cutters and related tables are rebaseCompanies and rebaseRefs.
The cutters table only gives information about the sequences that are
recognized and cut by these enzymes. The actual mappings of the sequences
to the genome are done on the fly so they are not available in any of our
databases.

It is possible for you to create the mappings of restriction
enzymes to a genome sequence yourself using programs developed by the
UCSC Genome Browser group. Our source code is open source and freely
available to non-commercial users.

http://genome.ucsc.edu/FAQ/FAQlicense#license3

You can either use the whole genome in a 2bit file created by using
the faToTwoBit program or you can do this chrom by chrom using either
FASTA files of sequences or sequences in nib format:

ftp://hgdownload.cse.ucsc.edu/goldenPath/<assembly>/bigZips/chromFa.zip

OR

ftp://hgdownload.cse.ucsc.edu/../gbdb/<assembly>/nib/

where <assembly> is the database or assembly name e.g. hg18, mm8.

Then you need to put a restriction enzyme sequence in a FASTA file
(e.g. RE.fa) and run the oligoMatch program:

oligoMatch RE.fa chr1.nib /dev/stdout \
| sed 's/\(+[0-9]\+\)/<REname>/' > RE.bed

where <REname> is the name of the enzyme is in RE.fa.

This also works, and gets rid of negatives in the 4th column
(only relevant if search sequence is not palindromic):
oligoMatch RE.fa chr1.nib /dev/stdout \
| sed 's/[-\+][0-9]\+/<REname>/' > BstBI.bed

oligoMatch is in the src/hg/utils/oligoMatch directory of the Browser
source code. The output file is BED format and the description for that is
here:

http://genome.ucsc.edu/FAQ/FAQformat#format1

I hope that this helps you. Please let us know if you have further
questions.

Rachel

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--
Rachel Harte
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu