HMM based classification for conserved SNARE protein domains

by Marius Audenis, Leana Ortolani and Gabriel Chiche

Supervisor: Carlos Pulido Quetglas

Link to the presentation: https://unils-my.sharepoint.com/:p:/r/personal/marius_audenis_unil_ch/_layouts/15/Doc.aspx?sourcedoc=%7B3a03a6f1-e7b0-4099-977c-fb2a72924716%7D&action=edit&wdPreviousSession=05951c8f-6f64-d402-8f8d-a9743eda88ca

Introduction

The SNARE family proteins play a role in membrane fusion and can be involved in several processes such as neurotransmission. All of these proteins share a common motif, which we call SNARE. This motif is essential to form the SNARE complex, which mediates the fusion between a vesicle and a target membrane.

This protein family has already been classified into four main groups (Qa, Qb, Qc, R) which are also divided into subgroups. This classification informes about the function ans sub-cellular localization of the protein.

In this project, we aim to build an algorithm capable of automatically classifying a SNARE sequences, thus giving rapid and accurate insights about its function. The classification method will be based on HMM models. We will build one HMM per class,

Broad picture

The classification will be based on HMM models