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Old 02-08-2007, 08:06 AM   #1
cyz70
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bioinformatics software on Suse


Dear all,

I found some older thread about Suse's repositories in this forum searing good bioinformatics sites. Forum member Abisko00 was referring on biolinux.org site where are some pieces available... anyway biolinux itself is a kind a distro where everything like that is included by default and repositories are updated... nice but this is debian based stuff... seems some other communities have been active for fedora as well, ok both distros are potential for me as I'm slowly trying to quit Suse but at the moment ... Abisko00 or anybody else, any good suggestions for any "complete" compilations for Suse?! or still only rpmseek?

Actually I have an another urgent need, probably wrong audience but who knows, so any linux based package for reading BD FACS type flow cytometer files known?

cheers,
Cyz
 
Old 02-09-2007, 08:53 AM   #2
abisko00
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I found no recent repositories for SUSE. Biolinux.org seems to be down or reorganizing itself. I will try to post a collection of tools that work on my system (10.1) a little later. I don't know any software for the flow cytometer. Guess that's pretty specialized.

Last edited by abisko00; 02-09-2007 at 09:04 AM.
 
Old 02-11-2007, 01:32 PM   #3
cyz70
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yup, I forgot to mention that I use still suse 10.0 at the moment...

... and these bio-linux debian packages, I tried them on Kubuntu, yak! specifying repositories works fine BUT at least for me it resulted in several error messages while trying to install some of these pieces and finally I messed up my Kubuntu totally :-( I will give a try for Fedora rpm's next, hope it is better...
 
Old 02-11-2007, 02:17 PM   #4
abisko00
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Most of that stuff compiles quite well on SUSE (e.g. EMBOSS/JEMBOSS), some other runs with Java, so in most cases it's not necessary to have distro-specific packages. However, it depends on the piece you want to run. I wasn't able to compile ClustalX for example, but the pre-compiled binary works as well. The precompiled blast binaries run very well, and most of the NCBI toolbox compiles without problems. I can recommend FinchTV (binary) for sequence chromotograms (similar to Chromas). primer3 and clustalw can be used with the Jemboss interface.

Last edited by abisko00; 02-12-2007 at 03:25 AM.
 
Old 02-12-2007, 10:11 AM   #5
cyz70
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EMBOSS/JEMBOSS I have/had (some major crash happened some time ago)
ClustalX as well
FinchTV I use daily at the moment
Also I use ARB frequently...
Jaview etc... but the major problem for me... so far no anything equal to BioEdit, mostly I lack the handy sequence editor part, Seaview is the most similar what I need...

Also GDE stuff seems to be useful, but I did not get it running...maybe Jemboss interface is enough...
 
Old 02-12-2007, 10:43 AM   #6
abisko00
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To be honest...I work almost exclusively on Windows at the moment. I found BioEdit very nice, but currently use VectorNTI from Invitrogen. There's nothing comparable for Linux at the moment. But for primer design, I still use a combination of perlprimer and primer3 on Linux. With the help of people from this community, I wrote a script that feeds perlprimer data into primer3. A great combination!
 
Old 02-13-2007, 08:40 AM   #7
cyz70
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ok... my colleagues use VectorNTI as well... SeqLab (GCG package) over ssh tunnel from the server is kind a solution as a sequence editor...

but I foubd reasinable stuff for flow cytometry, Java stuff (which I do not like so much) but works!

who is interested
http://www.wehi.edu.au/cytometry/WEASELv2.html
 
  


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