Computational Predictions Of S/Mar Sites?
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9.7 years ago

Are there any computational predictions of S/MAR sites available in a format that can be visualized in a browser like Ensembl or UCSC Genome Browser?

ensembl sequence ucsc browser • 1.7k views
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3
Entering edit mode
9.7 years ago

A search of the DAS registry does not show anything and I do not know of a DB that stores this info.

However you can run marscan from the EMBOSS suite and export to gff. Then view this on the genome browser of your choice (e.g. attach the file in Ensembl under "manage your data").

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Entering edit mode
9.7 years ago

I don't think so. You could map accessions from S/MARtDB using e.g. blat: http://smartdb.bioinf.med.uni-goettingen.de/cgi-bin/SMARtDB/smar.cgi. Also have a look here for tips to other methods beyond the one suggested by Alistair.

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