Does someone know any program for in silico enzyme digestion. I am a web lab scientist , need to do a computational simulation for whole genome enzyme digestion. I need a program which has the input option for genome, enzyme, the resulting fragment size range, also whether the fragment is unique. The output file are something like the Bed file like format with chr, start, end, and fragment size etc. It will be great that it can also give a distribution plot for the fragment. Thanks a lot!!!! I will be really appreciate.
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This paper has a program for it but I don't know if it is available:
Zhou et al. J of Bacteriology 2004
http://jb.asm.org/cgi/content/abstract/186/22/7773 -
There is an instrument!
Hi -
The reference cited is the basis of an instrument that does this type of mapping made by OpGen. See OpGen.comComment
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Hi sunsnow86,
Did you manage to find thein-silico digestion software you were looking for? I'm looking for the same now.Comment
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Counting RE site in bigger genome
Dear sunsnow86 and fastidiousme,
Did you find somw tool/scripts to estimate restriction enzyme sites in bigger genomes? I am also looking for the same.
Regards,
SComment
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Probably multiple tools out there, but it is also a good project for a beginning bioinformatics student. Without excessive bells-and-whistles, should be about a page of code in any high-level language with good bioinformatics library support (e.g. Perl, Python, Java)Comment
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