software for generating a restriction map

[mmmm]

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?

[GenoMax]

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/

[mmmm]

thank you- what is the input file for the whole bacterial genome?

[GenoMax]

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.

[mmmm]

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?

[GenoMax]

Long as you can get those contigs/scaffolds in a supported format (say fasta), remap will work.

[mmmm]

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?

[mmmm]

do I have to get permission access as I do not have the admin right to the already installed software?

[GenoMax]

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.html