NDLI: A meta-genome sequencing and assembly preprocessing algorithm inspired by restriction site base composition

Content Provider	IEEE Xplore Digital Library
Author	Bonham-Carter, O. Ali, H. Bastola, D.
Copyright Year	2012
Description	Author affiliation: College of Information Science & Technology, School of Interdisciplinary Informatics, Peter Kiewit Institute, University of Nebraska, Omaha, NE USA (Bonham-Carter, O.; Ali, H.; Bastola, D.)
Abstract	Motivation: In meta-genome sequencing and assembly projects, where there are different types of contigs mixed together in a single pool, the task of assembling its different organisms is a complex and challenging problem. It is therefore desirable to sort the contigs by origins into separate bins from which to work. We propose a framework of using the base compositions of bacterial restriction sites to generate sets of motifs which work to differentiate organismal groups, including the contigs from those groups. We introduce spectrum sets and show how to strategically select them for use in binning contigs from different organisms. We suggest that this framework can save time during a meta-genome sequencing and assembly project. Results: Our method is able to differentiate organisms and to successfully determine the association of the contigs which were derived from an organism. In particular, we show that two genera are fundamentally different by analyzing their motif proportions. Using one of the four total spectrum sets, which encompass all known restriction sites, we show that different sets have different abilities to distinguish sequences. In addition, we show that the selection of a spectrum set which is relevant to one organism, but not the other, greatly improves performance of differentiation, even when the contig size is short (1000bps). Conclusions: Using ten trials of newly selected contigs to confirm our premise, our study provides a proof of concept for a novel and computationally effective method for a preprocessing step in meta-genome sequencing and assembly tasks.
Starting Page	696
Ending Page	703
File Size	1976519
Page Count	8
File Format	PDF
ISBN	9781467327466
e-ISBN	9781467327473
e-ISBN	9781467327442
DOI	10.1109/BIBMW.2012.6470222
Language	English
Publisher	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher Date	2012-10-04
Publisher Place	USA
Access Restriction	Subscribed
Rights Holder	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Subject Keyword	Microorganisms palindromes Heating Genomics DNA base composition restriction sites Bioinformatics Assembly spectrum sets
Content Type	Text
Resource Type	Article

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4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
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