Smart Sofatware for Restriction Analysis - multiple simultaneous restriction analysis... (Jul/07/2008 )

H3llo,

does anyone here have the knowledge of a computer program that would allow me to make in-silico digestion of multiple sequences simultaneously ? Even better, a software that would be able to tell me if a RE cuts in this sequence but not in another one, defined by the user...

thanks for the suggestions

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sorry I dont know.
Hope someone can help
you.

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Bioedit perhaps, don't needed and used the program very intensively.

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thanks hobglob, I never heard of it beofre, I'll give it a try

edit : unfortunately, it doesn't even inculde RE, Ig uess I'll stick to aPe with my simulated gels all over my screen ...

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Ph3no, I see you around, and so let me badger you with one more of those crawling links:

http://search.vadlo.com/b/q?sn=158621799&a...nzyme&rel=1

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It wouldn't be hard to write such a program in Perl, one that takes a fasta file containing multiple sequences and, referring to a list of enzyme recognition sites, tells you what cuts or doesn't cut and where.

Is that what you're looking for?

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Or you can use one of the many EMBOSS programs available for such things. See, for example, the webserver at Purdue University, or select a closer server from the SourceForge list.

For more information about the EMBOSS open source project, see here.

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Thank you homebrew.... I never saw this website... there are so many of them anyway... but it allows restriction analysis of multiple sequences...

thanks again

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EMBOSS is a wonderful set of programs -- I set up a Linux server running this suite for my lab. I also put the command-line programs on all the lab's Windows computers (see here).

There's also an associated group of programs called EMBASSY, which includes such things as MEME, and multiple sequence editor called MSE, the phylogeny package PHYLIP, et al. These packages are released under a different license than the programs comprising the EMBOSS package, and are also available at the EMBOSS site.

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I've found better, it's called in silico RFLP, but you can even do tRFLP (link)

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