Publication Details

digIS: automated pipeline for detecting distant, novel insertion sequence elements in prokaryotes

PUTEROVÁ Janka and MARTÍNEK Tomáš. digIS: automated pipeline for detecting distant, novel insertion sequence elements in prokaryotes. In: Data & Knowledge 2018. Brno: Brno University of Technology, 2018, pp. 1-5. ISBN 978-80-214-5679-2.
Czech title
digIS: automatická pipeline pro detekci vzdálených a nových inzerčních sekvencí u prokaryot
Type
conference paper
Language
english
Authors
Keywords
insertion sequence, hidden markov models, transposons, mobile genetic elements, transposase
Abstract
Insertion sequences (ISs) are short DNA elements (typically less than 5 kb) and represent the simplest transposable elements. They are widespread in prokaryotes and may occur in high numbers in their genomes. ISs play important role in prokaryotic genome structure and evolution, for example, they can cause large rearrangements in the host genome or gene inactivation. Current ISs annotation tools depend either on existing genome annotations or databases of known IS elements and lack generalization capability resulting in an inability to detect novel IS elements or distant members of individual IS families. Here we introduce a novel approach which tackles these shortcomings based on manually curated pHMMs.
Published
2018
Pages
1-5
Proceedings
Data & Knowledge 2018
Conference
Data a znalosti 2018, Brno, CZ
ISBN
978-80-214-5679-2
Publisher
Brno University of Technology
Place
Brno, CZ
BibTeX
@INPROCEEDINGS{FITPUB11813,
   author = "Janka Puterov\'{a} and Tom\'{a}\v{s} Mart\'{i}nek",
   title = "digIS: automated pipeline for detecting distant, novel insertion sequence elements in prokaryotes",
   pages = "1--5",
   booktitle = "Data \& Knowledge 2018",
   year = 2018,
   location = "Brno, CZ",
   publisher = "Brno University of Technology",
   ISBN = "978-80-214-5679-2",
   language = "english",
   url = "https://www.fit.vut.cz/research/publication/11813"
}
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