Improving prokaryotic transposable elements identification using a combination of de novo and profile HMM methods
Improving prokaryotic transposable elements identification using a combination of de novo and profile HMM methods
By Jonathan Filée
CNRS (2013)
Abstract Paper

Jonathan  Filée

CNRS

France

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These 3 pipelines are designed to find prokaryotic transposons as ISs and MITEs.
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August 28, 2013
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Python Python 2.7
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September 30, 2013
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Abstract
Background Insertion Sequences (ISs) and their non-autonomous derivatives (MITEs) are essential components of prokaryotic genomes inducing duplication, deletion, rearrangement or lateral gene transfers. Although ISs and MITEs are relatively simple and basic genetic elements, their detection remains a difficult task due to their remarkable sequence diversity. With the advent of high-throughput genome and metagenome sequencing technologies, the development of fast, reliable and sensitive methods of IS and MITEs detection become an important challenge. So far, almost all studies dealing with prokaryotic transposons have used classical BLAST-based detection methods against reference libraries. Here we introduce alternative methods of detection either taking advantages of the structural properties of the elements (de novo methods) or using an additional library-based methods using profile HMM searches. Results In this study, we have developed three different work flows dedicated to ISs and MITEs detection : the first two use de novo methods detecting either repeated sequences or presence of Inverted Repeats ; the third one use 28 in-house IS alignment profiles with HMM search methods. We have compared the respective performances of each methods using a reference dataset of 30 archaeal genomes in addition to simulated and real metagenomes. Compare to a BLAST-based method using ISFinder as library, de novo methods significantly improve IS and MITEs detection with the discovering of 30 news elements (+20%) in addition to the 141 multi-copies element already detected by the BLAST approach in the 30 archaeal genomes. Many of the new elements correspond to ISs belonging to unknown or highly divergent families. The total number of MITEs have even doubled with the discovering of elements displaying very limited sequence similarities with their respective autonomous partners (mainly in the Inverted Repeats of the elements). Concerning metagenomes, with the exception of short reads data (<300bp) where both techniques seem equally limited, profile HMM searches considerably ameliorate the detection of transposase encoding genes (up to +50%) generating low level of false positives compare to BLAST-based methods. Conclusion Compare to classical BLAST-based methods, the sensitivity of de novo and profile HMM methods developed in this study allow a better and more reliable detection of transposons in prokaryotic genomes and metagenomes. We believed that future studies implying ISs and MITEs identification in genomic data should combine at least one de novo and one library-based method, with optimal results obtain by running the two de novo methods in addition to a library-based search. For metagenomic data, profile HMM search should be favored, a BLAST-based step is only useful to the final annotation into groups and families.
Filée, J., "Improving prokaryotic transposable elements identification using a combination of de novo and profile HMM methods", CNRS.
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