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Showing posts from June, 2014

How to find domains on a protein sequence?

Probably  you have heard about blast. It helps to find homologous sequences, it can be use through different variants with proteins, genes or just partial sequences to try to find what it is. It can be used also for proteins but there is another tool which can compete with it: HMMER In this article I will describe how I used it to find which kind of protein do we have. HMMER, like blast, has a family of functionalities but it was originally thought as a tool to find homologous proteins through a Hidden Markov Model . At the date of publication has four main functionalities ( hmmsearch jackhmmer hmmscan phmmer ) that can be used online. I will center in hmmsearch, the main tool, which we can run locally after downloading the software, I assume in this post that you are working with a computer with some of the Linux distributions and that you already downloaded the HMMER software and installed it. (See the manual ) Setps We need a profile of Hi