Suggested tool for protein analysis? - (Jan/05/2008 )
I'm going to compare obtained sequences of a gene obtained by RACE-cloning from different species, and I want to compare their predicted protein sequence using some kind of analysis tool, maybe online?
I'm not familiar to any tool of this kind - does anyone have a program to recommend a beginner?
Thanx
I'm not familiar to any tool of this kind - does anyone have a program to recommend a beginner?
Thanx
I mean that I want to try to compare their 3D-structure
Have a look at the expasy-website expasy . There are all tools you will need for prediction of posttranslational modifications, homology and structure and alignement.
swiss-model is the right tool for tertiary structure prediction (swiss-model. BUT: You will need a the structure of a similar protein with experimentally derived structure for moedling, as far as i know. Always keep in mind, that computational tertiary structures are only predictions!
I think comparing computational predicted structures is no good way. The first step should be to align your aa-sequences (e.g. with CLUSTALW). Find out which domains are conserved and which aa could be important for structure and/or catalytic activity!
this could also be helpful Evolutionary trace server...
swiss-model is the right tool for tertiary structure prediction (swiss-model. BUT: You will need a the structure of a similar protein with experimentally derived structure for moedling, as far as i know. Always keep in mind, that computational tertiary structures are only predictions!
I think comparing computational predicted structures is no good way. The first step should be to align your aa-sequences (e.g. with CLUSTALW). Find out which domains are conserved and which aa could be important for structure and/or catalytic activity!
Thank you! I've actually looked at expasy and thought I might use it. I have cloned the gene in a fish, and will compare it to the known zebrafish-sequence from NCBI. I have some mutations in "my" gene compared to the zebrafish gene, and I want to look at the proteins in 3D to see if the mutations give a different structure or not, and things like that. I found a tutorial for deepview - maybe I should read that one and try to figure out the next step.