Scalability and accuracy improvements of consistency-based multiple sequence alignment tools

Authors:
Miquel Orobitg;Jordi Lladós;Fernando Guirado;Fernando Cores;Cedric Notredame
Affiliations:
Universitat de Lleida, Lleida, Spain;Universitat de Lleida, Lleida, Spain;Universitat de Lleida, Lleida, Spain;Universitat de Lleida, Lleida, Spain;Universitat Pompeu Fabra, Barcelona, Spain
Venue:
Proceedings of the 20th European MPI Users' Group Meeting
Year:
2013

Citing 6
Cited 0

Probalign: multiple sequence alignment using partition function posterior probabilities

Bioinformatics
Cloud-Coffee

Bioinformatics
MSAProbs

Bioinformatics
Exploiting parallelism on progressive alignment methods

The Journal of Supercomputing
Enhancing the Scalability of Consistency-based Progressive Multiple Sequences Alignment Applications

IPDPS '12 Proceedings of the 2012 IEEE 26th International Parallel and Distributed Processing Symposium
Improving multiple sequence alignment biological accuracy through genetic algorithms

The Journal of Supercomputing

Quantified Score

Hi-index	0.00

Visualization

Abstract

Multiple sequence alignment (MSA) is one of the most useful tools in bioinformatics. However, the growth of sequencing data imposes further difficulties for aligning it with traditional tools. For large-scale alignments with thousands of sequences it will be necessary to use and take profit of the high performance computing (HPC). This paper, focused on the consistency-based T-Coffee MSA tool, presents several innovative solutions with the objective of improving its efficiency, scalability and accuracy. The results obtained show that our approach doubles the speed-up of the progressive alignment, thus allowing T-Coffee to align twice as many sequences while also improving the alignment accuracy.