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Pregled bibliografske jedinice broj: 509332

Alignment-free detection of local similarity among viral and bacterial genomes

Domazet-Lošo, Mirjana; Haubold, Bernhard
Alignment-free detection of local similarity among viral and bacterial genomes // Bioinformatics, 27 (2011), 11; 1466-1472 doi:10.1093/bioinformatics/btr176 (međunarodna recenzija, članak, znanstveni)

CROSBI ID: 509332 Za ispravke kontaktirajte CROSBI podršku putem web obrasca

Naslov
Alignment-free detection of local similarity among viral and bacterial genomes

Autori
Domazet-Lošo, Mirjana ; Haubold, Bernhard

Izvornik
Bioinformatics (1367-4803) 27 (2011), 11; 1466-1472

Vrsta, podvrsta i kategorija rada
Radovi u časopisima, članak, znanstveni

Ključne riječi
alignment-free method; local sequence homology; genome comparison; HIV; horizontal gene transfer; suffix tree; suffix array; shortest unique substring

Sažetak
Motivation: Bacterial and viral genomes are often affected by horizontal gene transfer observable as abrupt switching in local homology. In addition to the resulting mosaic genome structure, they frequently contain regions not found in close relatives, which may play a role in virulence mechanisms. Due to this connection to medical microbiology, there are numerous methods available to detect horizontal gene transfer. However, these are usually aimed at individual genes and viral genomes rather than the much larger bacterial genomes. Here we propose an efficient alignment-free approach to describe the mosaic structure of viral and bacterial genomes, including their unique regions. Results: Our method is based on the lengths of exact matches between pairs of sequences. Long matches indicate close homology, short matches more distant homology, or none at all. These exact match lengths can be looked up efficiently using an enhanced suffix array. Our program implementing this approach, alfy (ALignment-Free local homologY), efficiently and accurately detects recombination break points in simulated DNA sequences and among recombinant HIV-1 strains. We also apply alfy to Escherichia coli genomes where we detect new evidence for the hypothesis that strains pathogenic in poultry can infect humans. Availability: alfy is written in standard C and its source code is available under the GNU General Public License from http://guanine.evolbio.mpg.de/alfy/. The software package also includes documentation and example data.

Izvorni jezik
Engleski

Znanstvena područja
Biologija, Računarstvo



POVEZANOST RADA

Projekti:
036-0361983-2012 - Semantička integracija heterogenih izvorišta podataka (Baranović, Mirta, MZO ) ( CroRIS)

Ustanove:
Fakultet elektrotehnike i računarstva, Zagreb

Profili:

Avatar Url Mirjana Domazet Lošo (autor)

Poveznice na cjeloviti tekst rada:

doi bioinformatics.oxfordjournals.org

Citiraj ovu publikaciju:

Domazet-Lošo, Mirjana; Haubold, Bernhard
Alignment-free detection of local similarity among viral and bacterial genomes // Bioinformatics, 27 (2011), 11; 1466-1472 doi:10.1093/bioinformatics/btr176 (međunarodna recenzija, članak, znanstveni)
Domazet-Lošo, M. & Haubold, B. (2011) Alignment-free detection of local similarity among viral and bacterial genomes. Bioinformatics, 27 (11), 1466-1472 doi:10.1093/bioinformatics/btr176.
@article{article, author = {Domazet-Lo\v{s}o, Mirjana and Haubold, Bernhard}, year = {2011}, pages = {1466-1472}, DOI = {10.1093/bioinformatics/btr176}, keywords = {alignment-free method, local sequence homology, genome comparison, HIV, horizontal gene transfer, suffix tree, suffix array, shortest unique substring}, journal = {Bioinformatics}, doi = {10.1093/bioinformatics/btr176}, volume = {27}, number = {11}, issn = {1367-4803}, title = {Alignment-free detection of local similarity among viral and bacterial genomes}, keyword = {alignment-free method, local sequence homology, genome comparison, HIV, horizontal gene transfer, suffix tree, suffix array, shortest unique substring} }
@article{article, author = {Domazet-Lo\v{s}o, Mirjana and Haubold, Bernhard}, year = {2011}, pages = {1466-1472}, DOI = {10.1093/bioinformatics/btr176}, keywords = {alignment-free method, local sequence homology, genome comparison, HIV, horizontal gene transfer, suffix tree, suffix array, shortest unique substring}, journal = {Bioinformatics}, doi = {10.1093/bioinformatics/btr176}, volume = {27}, number = {11}, issn = {1367-4803}, title = {Alignment-free detection of local similarity among viral and bacterial genomes}, keyword = {alignment-free method, local sequence homology, genome comparison, HIV, horizontal gene transfer, suffix tree, suffix array, shortest unique substring} }

Časopis indeksira:


  • Current Contents Connect (CCC)
  • Web of Science Core Collection (WoSCC)
    • Science Citation Index Expanded (SCI-EXP)
    • SCI-EXP, SSCI i/ili A&HCI
  • Scopus
  • MEDLINE

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