Can someone point us towards analysis software that is able to identify closely related protein sequences in a protein database through a comparison with a base target protein sequence?
Dr. Panda; thanks for answering my question. The base target protein sequence is a short amino acid sequence. We want to search protein databases against this short sequence. This is not our area of expertise. Given that, which of the programs you listed would be the best for our purposes? BLASTP and PSI-BLAST are variations of the same program I believe. Would BLASTP be better for what we want?