A little help on bioinformatics - (Oct/15/2008 )
I have been given the protein sequence for an uncultivated organism and I have been asked to use bioinformatics to produce a report on it:
I have done primary sequence analysis e.g. extinction coefficient, MW etc but I am really stuck on how to find out the domain structure of the protein, whether and ligands bind its it possible strucutre and function. I would like to know how to carry out these tasks rather than have the answer handed to me, as that is not neccessary.
Thanks for any help! I did get a bioinformatics book but it told me about the history of the subject not the programs and their applications.
Follow some of the links on the Entrez webpage for many useful bio-informatics stuff. Often they will tell you how they work in the FAQs pages.
i'd recommend you to visit wikipedia and look for blast. good luck.
Look here at expasy, there are many tools for protein sequence identification and domain analysis, just try them out.
Thanks expasy was really helpful. I was just a little confused with all the programs but the help section sorted which was which. I checked out the othersite as well which was great. Much appreciated.
Do a protein blast from here.
It will even tell you what protein it might be
with the conserved domains included in the analysis
the % similarity of the protein to other known homolog or ortholog