Published online 13 January 2005
Methods Online |
Detection and characterization of horizontal transfers in prokaryotes using genomic signature
INSERM U 494, 91 bd de l'Hôpital 75013 Paris, France
*To whom correspondence should be addressed. Tel: 33 1 44 27 77 12; Fax: +33 1 43 26 38 30; Email: deschavanne{at}ebgm.jussieu.fr
Received July 9, 2004. Revised November 22, 2004. Accepted December 10, 2004.
Horizontal DNA transfer is an important factor of evolution and participates in biological diversity. Unfortunately, the location and length of horizontal transfers (HTs) are known for very few species. The usage of short oligonucleotides in a sequence (the so-called genomic signature) has been shown to be species-specific even in DNA fragments as short as 1 kb. The genomic signature is therefore proposed as a tool to detect HTs. Since DNA transfers originate from species with a signature different from those of the recipient species, the analysis of local variations of signature along recipient genome may allow for detecting exogenous DNA. The strategy consists in (i) scanning the genome with a sliding window, and calculating the corresponding local signature (ii) evaluating its deviation from the signature of the whole genome and (iii) looking for similar signatures in a database of genomic signatures. A total of 22 prokaryote genomes are analyzed in this way. It has been observed that atypical regions make up 
6% of each genome on the average. Most of the claimed HTs as well as new ones are detected. The origin of putative DNA transfers is looked for among 12 000 species. Donor species are proposed and sometimes strongly suggested, considering similarity of signatures. Among the species studied, Bacillus subtilis, Haemophilus Influenzae and Escherichia coli are investigated by many authors and give the opportunity to perform a thorough comparison of most of the bioinformatics methods used to detect HTs.
Present address: Patrick Deschavanne, Equipe de Bioinformatique Génomique et Moléculaire (EBGM), INSERM E 03-46, Université Paris 7, case 7113, 2 place JUSSIEU, 75251 Paris Cedex 05, France
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