[BiO BB] (no subject)

[Bossers, Alex]

Amir,
nice going.
I wondered what your initial use case was before you started the project?

Some rapid remarks by just browing the manual;
  - having to remove Fasta headers? are you serious? A cmdline tool like yours is build to use many sequences right? Skipping headers or stripping some usefull info from it would be the first to fix.
- It analyses 4 and 6 mers.... what about the other enzymes also having cleavage outside the recognition sequences? 4-6 simple enzymes can be done with a single regexp.
- What about methylation dam/dcm and/or CpG in eukaryotes?

Looong time ago we made an online tool for such a thing as this using the complete REBASE 3700+ enzymes. We started with a proper use-case and requirements analysis. you might be able to get some ideas from that if they overlap.
You can find it here:
http://biolinux.smith.man.ac.uk/~campus13ab/ToolREA/

Good luck.

Alex
________________________________________
Van: bbb-bounces at bioinformatics.org [bbb-bounces at bioinformatics.org] namens amir chaouki [chaouki.amir at gmail.com]
Verzonden: vrijdag 21 januari 2011 16:10
Aan: bbb at bioinformatics.org
Onderwerp: [BiO BB] (no subject)

hello, i am a member in bioinformatics organisation and i
have created a new tool, named gCut, for restriction analysis
and i will appreciate if you can just check it and tell me
what you think about it, i have posted it in
bioinformatics.org but i just need some body with a lot of
experience in this field to tell me what he thinks about
this. you can find it in: gcut.sourceforge.net
please help me i will be grateful if you respond to this
message. thank you, tell me also what are the functionalities that i can add
in the future.
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