Les séminaires ont lieu sur le Campus Montpellier SupAgro/INRA de La Gaillarde (2, place P. Viala Montpellier)

Lundi 3 juin à 14h00 – Amphi 208 (Coeur d’Ecole)

Ramanathan Sowdhamini

National Centre for Biological Sciences, GKVK Campus, Bellary Road, Bangalore 560065, India
Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
Institute of Bioinformatics and Applied Biotechnology, Bangalore 560100, India

Cascaded sequence searches and artificial sequences for improved remote homology detection

Due to distant evolutionary connections between protein families, it might be hard to recognize them through simple sequence searches in computational approach. One can resort to intermediate sequences to facilitate such connections. I will describe how, in cases where two protein families are far apart in sequence space, cascaded sequence searches and computationally designed sequences can be introduced to facilitate connections. As expected, sequence coverage improves dramatically in cascaded sequence searches and after the introduction of computationally designed sequences between protein families. Repetitive cascaded sequence search approach was employed to improve the chances of difficult connections by means of intermediate sequences (Sandhya et al., 2005). Interestingly, several unexpected but convincing connections between families could be recognised in a round-about manner after including designed sequences (Mudgal et al., 2014). Such studies enable effective usage of sequence search algorithms in function annotation and also provide a glimpse of evolutionary lineages in connecting proteins in the sequence space.