@inproceedings{34c35271fc034c7eabbb248d221ed541,
title = "CRISPR detection from short reads using partial overlap graphs",
abstract = "Clustered regularly interspaced short palindromic repeats (CRISPR) are structured regions in bacterial and archaeal genomes, which are part of an adaptive immune system against phages. Most of the automated tools that detect CRISPR loci rely on assembled genomes. However, many assemblers do not successfully handle repetitive regions. The first tool to work directly on raw sequence data is Crass, which requires that reads are long enough to contain two copies of the same repeat. We developed a method to identify CRISPR repeats from a raw sequence data of short reads. The algorithm is based on an observation differentiating CRISPR repeats from other types of repeats, and it involves a series of partial constructions of the overlap graph. A preliminary implementation of the algorithm shows good results and detects CRISPR repeats in cases where other tools fail to do so.",
keywords = "CRISPR Detection, Filtering, K-mer counting, Overlap graph, Partial overlap graph, Sampling",
author = "Ilan Ben-Bassat and Benny Chor",
note = "Publisher Copyright: {\textcopyright} Springer International Publishing Switzerland 2015.; 19th Annual International Conference on Research in Computational Molecular Biology, RECOMB 2015 ; Conference date: 12-04-2015 Through 15-04-2015",
year = "2015",
doi = "10.1007/978-3-319-16706-0\_3",
language = "אנגלית",
series = "Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)",
publisher = "Springer Verlag",
pages = "16--27",
editor = "Przytycka, \{Teresa M.\}",
booktitle = "Research in Computational Molecular Biology - 19th Annual International Conference, RECOMB 2015, Proceedings",
address = "גרמניה",
}