BOCS: DNA k-mer content and scoring for rapid genetic biomarker identification at low coverage
نویسندگان
چکیده
منابع مشابه
K-mer Content, Correlation, and Position Analysis of Genome DNA Sequences for the Identification of Function and Evolutionary Features
In genome analysis, k-mer-based comparison methods have become standard tools. However, even though they are able to deliver reliable results, other algorithms seem to work better in some cases. To improve k-mer-based DNA sequence analysis and comparison, we successfully checked whether adding positional resolution is beneficial for finding and/or comparing interesting organizational structures...
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SUMMARY Counting all the k-mers (substrings of length k) in DNA/RNA sequencing reads is the preliminary step of many bioinformatics applications. However, state of the art k-mer counting methods require that a large data structure resides in memory. Such structure typically grows with the number of distinct k-mers to count. We present a new streaming algorithm for k-mer counting, called DSK (di...
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It is well acknowledged that alternative splicing module plays a crucial role to identify the variations of the RNA transcriptomes. In high-throughput short-read RNA, splicing analysis is a challenging task due to the uncertainty and time complexity of reads alignments onto genome and transcriptome. In this paper, we introduce k-mer based statistical method for splicing event analysis. The k-me...
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ژورنال
عنوان ژورنال: Computers in Biology and Medicine
سال: 2019
ISSN: 0010-4825
DOI: 10.1016/j.compbiomed.2019.05.022