alexa SlopMap: A Software Application Tool for Quick and Flexible Identification of Similar Sequences Using Exact K-Mer Matching
ISSN: 2153-0602

Journal of Data Mining in Genomics & Proteomics
Open Access

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Research Article

SlopMap: A Software Application Tool for Quick and Flexible Identification of Similar Sequences Using Exact K-Mer Matching

Ilya Y Zhbannikov1*, Samuel S Hunter1,2, Matthew L Settles1,2 and James A Foster1,2,3

1Institute for Bioinformatics and Evolutionary Studies, University of Idaho, USA

2The Institute of Bioinformatics and Evolutionary Studies (IBEST), University of Idaho, USA

3Department of Biological Sciences, University of Idaho, USA

*Corresponding Author:
Ilya Y Zhbannikov
Institute for Bioinformatics and Evolutionary Studies
University of Idaho, USA
Tel: 208-885-6010
E-mail: [email protected]

Received date: May 07, 2013; Accepted date: June 24, 2013; Published date: July 02, 2013

Citation: Zhbannikov IY, Hunter SS, Settles ML, Foster JA (2013) SlopMap: A Software Application Tool for Quick and Flexible Identification of Similar Sequences Using Exact K-Mer Matching. J Data Mining Genomics Proteomics 4:133.doi: 10.4172/2153-0602.1000133

Copyright: © 2013 Zhbannikov IY, et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

 

Abstract

With the advent of Next-Generation (NG) sequencing, it has become possible to sequence an entire genome quickly and inexpensively. However, in some experiments one only needs to extract and assembly a portion of the sequence reads, for example when performing transcriptome studies, sequencing mitochondrial genomes, or characterizing exomes. With the raw DNA-library of a complete genome it would appear to be a trivial problem to identify reads of interest. But it is not always easy to incorpo-rate well-known tools such as BLAST, BLAT, Bowtie, and SOAP directly into a bioinformatics pipelines before the assembly stage, either due to in-compatibility with the assembler’s file inputs, or because it is desirable to incorporate information that must be extracted separately. For example, in order to incorporate flowgrams from a Roche 454 sequencer into the Newbler assembler it is necessary to first extract them from the original SFF files. We present SlopMap, a bioinformatics software utility which allows rapid identification similar to provided target sequences from either Roche 454 or Illumnia DNA library. With a simple and intuitive command-line interface along with file output formats compatible with assembly programs, SlopMap can be directly embedded in biological data processing pipeline without any additional programming work. In addition, SlopMap preserves flowgram information needed for Roche 454 assembler.

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