I actually have two queries. Biochemical studies suggested presence of an enzyme in an organism but the gene encoding the enzyme is not known. I would like to find out gene candidates based on homology search/sequence similarity, using sequences of similar enzymes present in other organisms. My questions are:
1. What points should I consider to select an already known gene/protein for use in homology search
2. To find out the orthologue of the known gene/prtoein by bioinformatics, which database/software should I use?
Please suggest papers/websites/softwares for beginners.
Thanks!
1. It is recommended that you use genes / proteins in which the functionality has been verified using a database of nearby species for which there is information.
2. You can use the NCBI database to obtain the complete sequence of the genes or use the InterPro database to obtain the domains(Recommendable). Then align your sequences with one of the two databases using BLAST.
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