I am interested to study Metabolic engineering and Bioinformatic subject. I want to work on the molecular mechanisms of the microbes found in extreme environments (extremophiles). In this regard, can anyone help in knowing some of the important and advanced tools/software to gain more knowledge in the subject?
I need your help and guidance. Thank you.
for constructung networks
Pathologic
KAAS on KEGG or BioCyc
you may also need to be familiar with SBML
for visualizing metabolic networks you may use
Cytoscape and cytoseed
for reaction networks you may use
CellNetAnakyzer
GLAMM
Vanted
Arcadia-Jdesigner , Celldesigner, Cell illustrator
if you are familiar with SBOL you might be interrested in
TinkerCell and GenoCAD
for flux balance analysis
FBA
COBRA 2.0
Optflux
in e.coli
http://www-shimizu.ist.osaka-u.ac.jp/shimizu_lab/FastPros/
for pathway analysis
IMG- Integrated micorbila genomes
COPASI
for culture
GrowMatch
Dear Sandeep.
All above is good. Also, you can try IPA Qiagen. It is not free but grea.
Dear Mohammad, Martin and Shahrooz - thank you very much. It will help be a lot.
What are you investigating specifically? Is it promoters, transcription factors, gene sequence or metabolic pathways?
Check the following:
Galaxy Servers: https://usegalaxy.org/
Elixir: https://www.elixir-europe.org/
Bioinformatics.ca
Have a glance on this article Article Computational Tools for Metabolic Engineering
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