Your set of bio-info tools and why it's great :)

[ptr200]

Hello everyone!

I've found this forum as I was looking for a good (and preferably free) bio-info tool, or even whole set of such tools.

Despite the fact that I haven't yet found anything that could replace/expand my usual set consisting of APE and NEBCutter , I thought I could ask you WHAT IS YOUR FAVOURITE BIO-INFO TOOL?

Few additional words of explanation and maybe a brief overview of what you use this software for would be nice.

Thanks for help!

[PVsnyper]

ok does anyone know any software for "Response Surface Methodology" free to download and full version or atleast the most part that we can have

[Omicron Lyrae]

Hmm, there are so many bioinformatics tools out there you can't count them anymore. So maybe your question should be more specific or sub grouped into the purpose of the tool. Beside that my favorites are:

Geneoius (tool for DNA Manipulation, Primer Design, Seq. Alignment, Restriction & Cloning

[Omicron Lyrae]

Ohh wrong Button pushed...

I like Geneoius because its easy to handle and manipulation and overwiewing lots of data (Primer Creation) is quite fast. Okay next one:

Primer Blast(Web-based on NCBI): Allows of quick Specifity check, but it doesn't allow max 5' Stability settings, so I don't prefer it for Primer Creation.

Oligo Explorer: A bit old and doesn't support melting temperature calculation after Santa Lucia, but has the great possibility to control Primer-Dimer and Hairpins directly visual (Alignment scores got not an absolute evidence) and calculates (after Breslauer et. al) the melting temperatures of Dimer/Hairpin structures.

Copasi: Great tool for analyzing biochemichal networks. Provides both, stochastical Calculations and deterministic calculations based on differential equation. Ist one of the seldom all in one analyzing and simulation tools for systems biology.

Celldesigner: A biochemical network visualization and analysing/simulation tool. Can be used with Copasi together (seperate or through SBW).

Cytoscape: Primary used as visualization tool. Highly modifyable through plugins. Very good visualization possibilities.

Not direct tools, but support software:

SBML(systems biology markup language): Hope this will be the total standard in nearest future, so theres no need for so many conversions for different filetypes (some are just for visualization, some are just for kinetis equations,...) because in SBML theres all in one.

SBW(Systems biology Workbech): Creates good Connectivity between different programs (like Copasi and Celldesigner), so there is a good workflow guaranteed.

R and Rapid Miner should be mentioned, but I'm not sure, if they belong here.

I think it's enough for the first time. Maybe I got another idea later...

[jmcelh]

Howdy folks,
Do any of you know of any software that can produce predicted quaternary structure models from my 3D monomeric structures? I used SWISS-MODELLER to generate the monomeric forms but it won't generate the dimeric functional form. I was thinking there has to be something that queries PDB using my locally generated .PDB file.

As for useful programs, I had tried to link in a URL here to containing a small directory of useful bioinformatics resources but it wouldn't let me post with it (it can be found at bioinformatics.ca i will try post it when i have made two more posts (apparently then it will let me).


But i would really appreciate any software you guys could suggest for my problem.

Best Wishes,

Mac