restriction mapping

[Mike Quail]

Hi

I am currently looking to isolate restriction fragments that cover gaps that are left in several genomes. To do this I need to cut the sequence we have of a genome with all known database enzymes and then select those that just cut a few times and in the right place so as to excise the region of the genome I require. 

GCG programs map and mapplot were excellent for doing this. Map in particular is good as it gives a graphical plot for each enzyme (one enzyme per line) plotting all the enzymes on a page or two so you can rapidly see which is appropriate.

I have tried the EMBOSS programs and basically they are no use. REMAP does what I want but in too great detail (the output would stretch round the globe) and RESTRICT is too unordered in its output. 

I have got a program called oligo on my PC that will do this, BUT it has problems with big sequences. Recently I tried analysing a 1.5Mb chromosome and it would only work if I limited the number of enzymes to 6 or less. So I could transfer the data over to my PC and try with that but as this organism is 5Mb it will be very slow going.

Have you any ideas of how this could be done in EMBOSS.

M.Quail



Project Leader

Wellcome Trust Sanger Institute

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