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: [email protected] [[email protected]] namens amir chaouki [[email protected]] Verzonden: vrijdag 21 januari 2011 16:10 Aan: [email protected] 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. _______________________________________________ BBB mailing list [email protected] http://www.bioinformatics.org/mailman/listinfo/bbb _______________________________________________ BBB mailing list [email protected] http://www.bioinformatics.org/mailman/listinfo/bbb
