Extracting Protein Sequences

Question

[Hari]

Hi, I am trying to extract all the protein sequences of Rho Gef in humans,i need to avoid redundancy and also extract all the sequences.How do i achieve this? I have already tried it with Uniprot but I how can i check if all the sequences are complete,valid and also non-redundant.Is there a way to do it automatically?

Thank you very much

Answer 1

[Chris]

As for 'non-redundant', this depends on your desired level of redundancy. One measure is sequence identity, i.e. throw away each sequence that already has a homolgue (as defined by a identity threshold) in the set. CD-HIT is one of the most popular tools.

[Hari]

Thanks for your response,how to do i know if i have all the sequences of Rho gef ? by redundancy i mean i want all the sequences in human but not homologs or repeats but at the same time not exclude any other sequence..

[Hari]

Hi CD hit is really useful,I download all the given protein sequences for RhoGef and cluster them in groups and the non similar or irrevelant proteins are filtered out by this process.Is this correct approach?