I am looking for an easy and good software that can be used for performing an in silico restriction digestion of the whole genome DNA in order to generate a restriction map and identifying restriction sites removing non essential genomic sequences- is there a software for this purpose please?
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Not sure if this would work with a genome/chromosome sized data but you can give it a try: http://emboss.open-bio.org/rel/dev/apps/remap.html
You will of course need to install EMBOSS from here: ftp://emboss.open-bio.org/pub/EMBOSS/ -
thank you- what is the input file for the whole bacterial genome?Comment
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Emobss takes one of the following formats: http://emboss.sourceforge.net/docs/t...ormats.html#in
You probably have Fasta/Genbank. Which would be fine.Comment
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I want to run "remap" on the denovo assembled NGS reads (contigs/ scaffolds)- not complete fasta sequence- is this possible by emboss?- or is there another software for this?Comment
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Long as you can get those contigs/scaffolds in a supported format (say fasta), remap will work.Comment
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thanks- have tried
$ remap -notran -sbeg 1 -send 60
and entered the multi fasta input file (scaffolds.new) but have got "cannot locate enzyme file- run rebaseextract"
does this mean that rebasedatabase is not installed within emboss?
but when I wrote rebaseextract- I got "rebase database within refm file"-????- so how could I access that file?Comment
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do I have to get permission access as I do not have the admin right to the already installed software?Comment
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You should be able to run the rebaseextract in your own directory: http://emboss.sourceforge.net/apps/r...seextract.html
You will find the "proto" and "withref" files for REBASE here: http://rebase.neb.com/rebase/rebase.files.htmlComment
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