Kudos......

Hangdog42 · 08-12-2004, 08:10 PM

I haven't had time to play with DNALinux as much as I would like, but it looks like a nicely done distro. If you're looking for suggestions for a few additional tools to add, here is my list:

sim4 - VERY useful for defining exon/intron boundaries
GrailEXP and/or Genscan for gene hunting
Repeat Masker

sbassi · 08-13-2004, 09:30 AM

Quote:

Originally posted by Hangdog42
I haven't had time to play with DNALinux as much as I would like, but it looks like a nicely done distro. If you're looking for suggestions for a few additional tools to add, here is my list:
sim4 - VERY useful for defining exon/intron boundaries
GrailEXP and/or Genscan for gene hunting
Repeat Masker

Thank you for you comments and suggestions.
Sim4 was added in the dev version and will be in the next release (past 0.36, since 0.36 it is in the way to be uploaded).
Genscan licence doesn't allow redistribution, look here:

Quote:

RECIPIENT agrees to use the Program solely for internal purposes
and shall not distribute or transfer it to another location or to
any other person without prior written permission from STANFORD.

GrailEXP is in the same situation:

Quote:

5. RECIPIENT agrees to use the Program solely for internal purposes
and shall not distribute or transfer it to another location or to
any other person without prior written permission from UT/BATTELLE.

RepeatMasker: The download file is not available in their website, I had to complete a form and I am now waiting for their response.

Hangdog42 · 08-13-2004, 02:55 PM

Yeah, I thought about the licensing problems after I posted. Quite frankly, too much bioinformatics software has restrictions like this. I think a lot of the people who write this stuff only give lip service to the idea of open source software. They are all for everyone else's software being open source, but want all sorts of restrictions around theirs.

Thanks for the update, I'll look forward to the next version.