Why can rare-cutters (like Not1no longe r be used
Pieter J. de Jong
I noticed that newer versions of the Genome Browser have been changed with respect to “restriction enzymes”. Many of the commonly used “rare cutters” in mammalian genomes have multiple CpG dinucleotides and/or are >longer than 6 bp. Very common enzymes (e.g. Not1, AsiSI) can now only be analyzed for segment below 20 kb. As you know, Not1 occurs about once per million bp and it would be hard to quickly analyze UCSC-displayed BAC clones for internal Not1 sites. It is a bit painful having to download the sequence frequently and then analyze by custom software. Would it be possible that add some or many of the rare cutters again to the list for zoom level up to 250,000 bp (preferably a larger zoom level)?
Pieter J. de Jong
Pieter J. de Jong
I just discovered that the hg38 (Human) browser still allows many more enzymes to be analyzed in the zoom window up to 250kb, whereas the mouse mm9 and mm10, do not permit this.
Pieter de Jong
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Matthew Speir
Thank you for your question about the "Restriction Enzymes" track in the UCSC Genome Browser.
I'm unable to replicate the issue with the Restriction Enzymes track not loading above 20,000 bp for the mm10/mm9 genomes. Here is a session with the track turned on with the NotI enzyme entered and displayed at a region of ~226,000 bp:
https://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=mspeir&hgS_otherUserSessionName=mm10_restEnzover20kbp
Could you provide a session that shows the issue you are describing?
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Matthew Speir
UCSC Genome Bioinformatics Group
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