analysing protein sequences - How to find domains? (Apr/08/2008 )

hello, as part of my project i want to compare 2 protein sequences. I have access to the DNaStar software package , and have managed to align them with MegAlign and get the % similarity. What I would like to do is find domains of interest eg zinc binding domain. Can anyone tell me how to do this? I have tried using the protean section of DNAstar, but i cant seem to find what im looking for. Im in the middle of writing up my thesis and Ive never done anything remotely "bio-informatical" before so any advice would be greatly appreciated,
Thanks in advance

hello, as part of my project i want to compare 2 protein sequences. I have access to the DNaStar software package , and have managed to align them with MegAlign and get the % similarity. What I would like to do is find domains of interest eg zinc binding domain. Can anyone tell me how to do this? I have tried using the protean section of DNAstar, but i cant seem to find what im looking for. Im in the middle of writing up my thesis and Ive never done anything remotely "bio-informatical" before so any advice would be greatly appreciated,
Thanks in advance

...or expasy.ch

Pfam is good, too: http://www.sanger.ac.uk/Software/Pfam/

Thanks for all your help, the protein Im trying to analyse is rotavirus NSP1. Ive tried all of the suggested programs but they do not identify any motifs within the protein. I know there is definitely a zinc binding motif in there from reviewing the literature. Any more suggestions greatly appreciated

Hi,

maybe ebi-interpro provides your information:
http://www.ebi.ac.uk/interpro/ISpy?mode=single&ac=Q3ZK61

bw Markus