It is possible to find a series of softwares in the literature designed to help uncover molecules characteristics, I'm not sure exactly what is your objective but softwares like Blast2GO help us to find gene and proteins functions by showing us some key features like domains, structure, bio-ontology, localization, etc. Depending on the organism you are studding you can trust in the electronically transfered information from similar and close related organisms, in other cases, like organisms with no related organisms that are characterized, you will have to obtain laboratory evidences. Ultimately its important to have in mind that these softwares, in most cases, will not provide you definitive evidences of genes and proteins functions as most of the cases are examples of transference of information. It's possible that a given protein with a known function in a determined organism has a different or non canonical function in another organism.

If you have a protein structure, you can use the pocketfinder and if you have only sequences, you must be first blast and alignment based on its similarity with other proteins guess its possible active site.

1. What do you have? Gene sequence or Protein sequence?

2. If you start with gene sequence, you can use BLASTn, tBLASTn to find out the related nucleotide and protein sequences which gives you a basic idea about the gene. Then you can find the functional domain, active sites, transmembrane region, signal sequence of your protein sequence using many online software such as SMART (http://smart.embl-heidelberg.de/smart/set_mode.cgi?NORMAL=1), PROSITE (http://prosite.expasy.org/), depending on your need.

Hope this helps! All the Best!

Dear Felipe Leprevost, Javad Maleki, and Venkatesh Kumaresan

I would like to a knowledge you how much I appreciate your cooperation with me. Recall I' m very grateful for you .

Your' s sincerely

Ali A. Ibrahim