CoMSA: compression of protein multiple sequence alignment files

Bioinformatics
Sebastian DeorowiczAgnieszka Debudaj-Grabysz

Abstract

Bioinformatics databases grow rapidly and achieve values hardly to imagine a decade ago. Among numerous bioinformatics processes generating hundreds of GB is multiple sequence alignments of protein families. Its largest database, i.e. Pfam, consumes 40-230 GB, depending of the variant. Storage and transfer of such massive data has become a challenge. We propose a novel compression algorithm, CoMSA, designed especially for aligned data. It is based on a generalization of the positional Burrows-Wheeler transform for non-binary alphabets. CoMSA handles FASTA, as well as Stockholm files. It offers up to six times better compression ratio than other commonly used compressors, i.e. gzip. Performed experiments resulted in an analysis of the influence of a protein family size on the compression ratio. CoMSA is available for free at https://github.com/refresh-bio/comsa and http://sun.aei.polsl.pl/REFRESH/comsa. Supplementary data are available at Bioinformatics online.

References

Oct 13, 2011·Molecular Systems Biology·Fabian SieversDesmond G Higgins
Jan 19, 2013·Molecular Biology and Evolution·Kazutaka Katoh, Daron M Standley
Jul 3, 2013·Bioinformatics·Noah M DanielsBonnie Berger
Aug 24, 2013·Bioinformatics·Sebastian DeorowiczSzymon Grabowski
Oct 18, 2013·Bioinformatics·Armando J Pinho, Diogo Pratas
Nov 21, 2013·Algorithms for Molecular Biology : AMB·Sebastian Deorowicz, Szymon Grabowski
Apr 22, 2014·Bioinformatics·Lukasz Roguski, Sebastian Deorowicz
Dec 31, 2014·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Siavash MirarabTandy Warnow
Mar 31, 2015·PloS One·Luís M O MatosArmando J Pinho
Jul 8, 2015·PLoS Biology·Zachary D StephensGene E Robinson
Dec 18, 2015·Nucleic Acids Research·Robert D FinnAlex Bateman
Sep 28, 2016·Scientific Reports·Sebastian DeorowiczAdam Gudyś
Nov 1, 2016·Nature Methods·Ibrahim NumanagićS Cenk Sahinalp
Nov 1, 2017·Bioinformatics·Vida RavanmehrOlgica Milenkovic

❮ Previous
Next ❯

Citations

Feb 6, 2019·Interdisciplinary Sciences, Computational Life Sciences·Morteza HosseiniArmando J Pinho
Jun 22, 2019·Bioinformatics·Sebastian Deorowicz, Agnieszka Danek

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.