Recommended Conferences

Enzymology Molecular Biology

Chicago, USA

Adolescent Health Medicine

Dubai, UAE
 

Cgaln: fast and space-efficient whole-genome alignment

Author(s): Nakato R, Gotoh O

Abstract

Background: Whole-genome sequence alignment is an essential process for extracting valuable information about the functions, evolution, and peculiarities of genomes under investigation. As available genomic sequence data accumulate rapidly, there is great demand for tools that can compare whole-genome sequences within practical amounts of time and space. However, most existing genomic alignment tools can treat sequences that are only a few Mb long at once, and no state-of-the-art alignment program can align large sequences such as mammalian genomes directly on a conventional standalone computer.

Results: We previously proposed the CGAT (Coarse-Grained AlignmenT) algorithm, which performs an alignment job in two steps: first at the block level and then at the nucleotide level. The former is "coarse-grained" alignment that can explore genomic rearrangements and reduce the sizes of the regions to be analyzed in the next step. The latter is detailed alignment within limited regions. In this paper, we present an update of the algorithm and the open-source program, Cgaln, that implements the algorithm. We compared the performance of Cgaln with those of other programs on whole genomic sequences of several bacteria and of some mammalian chromosome pairs. The results showed that Cgaln is several times faster and more memory-efficient than the best existing programs, while its sensitivity and accuracy are comparable to those of the best programs. Cgaln takes less than 13 hours to finish an alignment between the whole genomes of human and mouse in a single run on a conventional desktop computer with a single CPU and 2 GB memory.

Conclusions: Cgaln is not only fast and memory efficient but also effective in coping with genomic rearrangements. Our results show that Cgaln is very effective for comparison of large genomes, especially of intact chromosomal sequences. We believe that Cgaln provides novel viewpoint for reducing computational complexity and will contribute to various fields of genome science.

Similar Articles

Whole-genome random sequencing and assembly of Haemophilus influenzae Rd

Author(s): Fleischmann RD, Adams MD, White O, Clayton RA, Kirkness EF, et al.

The automatic annotation of bacterial genomes

Author(s): Richardson EJ, Watson M

Microbial genome data resources

Author(s): Markowitz VM

The Genomes OnLine Database (GOLD) v

Author(s): Pagani I, Liolios K, Jansson J, Chen IM, Smirnova T, et al.

The automatic annotation of bacterial genomes

Author(s): Richardson EJ, Watson M

IMG: the Integrated Microbial Genomes database and comparative analysis system

Author(s): Markowitz VM, Chen IM, Palaniappan K, Chu K, Szeto E, et al.

The pangenome structure of Escherichia coli: comparative genomic analysis of E

Author(s): Rasko DA, Rosovitz MJ, Myers GS, Mongodin EF, Fricke WF, et al.

Efficient multiple genome alignment

Author(s): Höhl M, Kurtz S, Ohlebusch E

Versatile and open software for comparing large genomes

Author(s): Kurtz S, Phillippy A, Delcher AL, Smoot M, Shumway M, et al.

MicroScope: a platform for microbial genome annotation and comparative genomics

Author(s): Vallenet D, Engelen S, Mornico D, Cruveiller S, Fleury L, et al.

The pangenome structure of Escherichia coli: comparative genomic analysis of E

Author(s): Rasko DA, Rosovitz MJ, Myers GS, Mongodin EF, Fricke WF, et al.

Comparative analysis of two complete Corynebacterium ulcerans genomes and detection of candidate virulence factors

Author(s): Trost E, Al-Dilaimi A, Papavasiliou P, Schneider J, Viehoever P, et al.

The impact of next-generation sequencing on genomics

Author(s): Zhang J, Chiodini R, Badr A, Zhang G

Sequencing technologies and genome sequencing

Author(s): Pareek CS, Smoczynski R, Tretyn A

Basic local alignment search tool

Author(s): Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ

A primer on metagenomics

Author(s): Wooley JC, Godzik A, Friedberg I

Alignment of whole genomes

Author(s): Delcher AL, Kasif S, Fleischmann RD, Peterson J, White O, et al.

Analyzing patterns of microbial evolution using the mauve genome alignment system

Author(s): Darling AE, Treangen TJ, Messeguer X, Perna NT

Fast algorithms for large-scale genome alignment and comparison

Author(s): Delcher AL, Phillippy A, Carlton J, Salzberg SL

LAGAN and Multi-LAGAN: efficient tools for large-scale multiple alignment of genomic DNA

Author(s): Brudno M, Do CB, Cooper GM, Kim MF, Davydov E, et al.

High-throughput sequence alignment using Graphics Processing Units

Author(s): Schatz MC, Trapnell C, Delcher AL, Varshney A

The RAST Server: rapid annotations using subsystems technology

Author(s): Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, et al.

Genome visualization made fast and simple

Author(s): Gibson R, Smith DR

GenoMap, a circular genome data viewer

Author(s): Sato N, Ehira S

Visualization for genomics: the Microbial Genome Viewer

Author(s): Kerkhoven R, van Enckevort FH, Boekhorst J, Molenaar D, Siezen RJ

BacMap: an interactive picture atlas of annotated bacterial genomes

Author(s): Stothard P, Van Domselaar G, Shrivastava S, Guo A, O'Neill B, et al.

DNAPlotter: circular and linear interactive genome visualization

Author(s): Carver T, Thomson N, Bleasby A, Berriman M, Parkhill J

BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons

Author(s): Alikhan NF, Petty NK, Ben Zakour NL, Beatson SA

Circos: an information aesthetic for comparative genomics

Author(s): Krzywinski M, Schein J, Birol I, Connors J, Gascoyne R, et al.

Evaluation of invertebrate infection models for pathogenic Corynebacteria

Author(s): Ott L, McKenzie A, Baltazar MT, Britting S, Bischof A, et al.

The 160-kilobase genome of the bacterial endosymbiont Carsonella

Author(s): Nakabachi A, Yamashita A, Toh H, Ishikawa H, Dunbar HE, et al.

Bacterial pathogenomics

Author(s): Pallen MJ, Wren BW

Network-based prediction of protein function

Author(s): Sharan R, Ulitsky I, Shamir R

Conserved host-pathogen PPIs

Author(s): Barh D, Gupta K, Jain N, Khatri G, León-Sicairos N, et al.

Assigning protein functions by comparative genome analysis: protein phylogenetic profiles

Author(s): Pellegrini M, Marcotte EM, Thompson MJ, Eisenberg D, Yeates TO

Protein interaction maps for complete genomes based on gene fusion events

Author(s): Enright AJ, Iliopoulos I, Kyrpides NC, Ouzounis CA

How little do we actually know? On the size of gene regulatory networks

Author(s): Röttger R, Rückert U, Taubert J, Baumbach J

The microbial pan-genome

Author(s): Medini D, Donati C, Tettelin H, Masignani V, Rappuoli R

Genomics of Actinobacteria: tracing the evolutionary history of an ancient phylum

Author(s): Ventura M, Canchaya C, Tauch A, Chandra G, Fitzgerald GF, et al.

The pangenome structure of Escherichia coli: comparative genomic analysis of E

Author(s): Rasko DA, Rosovitz MJ, Myers GS, Mongodin EF, Fricke WF, et al.

Biogeography of the Sulfolobus islandicus pan-genome

Author(s): Reno ML, Held NL, Fields CJ, Burke PV, Whitaker RJ

Pathogenicity islands in bacterial pathogenesis

Author(s): Schmidt H, Hensel M

Burkholderia pseudomallei genome plasticity associated with genomic island variation

Author(s): Tumapa S, Holden MT, Vesaratchavest M, Wuthiekanun V, Limmathurotsakul D, et al.

The bacterial pan-genome:a new paradigm in microbiology

Author(s): Mira A, Martín-Cuadrado AB, D'Auria G, Rodríguez-Valera F

Toxin genes on pathogenicity islands: impact for microbial evolution

Author(s): Dobrindt U, Janke B, Piechaczek K, Nagy G, Ziebuhr W, et al.

PIPS: pathogenicity island prediction software

Author(s): Soares SC, Abreu VA, Ramos RT, Cerdeira L, Silva A, et al.

DNA relationships among some tox-bearing Corynebacteriophages

Author(s): Buck GA, Cross RE, Wong TP, Loera J, Groman N

The complete genome sequence and analysis of Corynebacterium diphtheriae NCTC13129

Author(s): Cerdeño-Tárraga AM, Efstratiou A, Dover LG, Holden MT, Pallen M, et al.

Bacterial genomics and pathogen evolution

Author(s): Raskin DM, Seshadri R, Pukatzki SU, Mekalanos JJ

Ribosomal multilocus sequence typing: universal characterization of bacteria from domain to strain

Author(s): Jolley KA, Bliss CM, Bennett JS, Bratcher HB, Brehony C, et al.

KAAS: an automatic genome annotation and pathway reconstruction server

Author(s): Moriya Y, Itoh M, Okuda S, Yoshizawa AC, Kanehisa M

AutoFACT: an automatic functional annotation and classification tool

Author(s): Koski LB, Gray MW, Lang BF, Burger G

Prodigal: prokaryotic gene recognition and translation initiation site identification

Author(s): Hyatt D, Chen GL, Locascio PF, Land ML, Larimer FW, et al.