RMI-DBG algorithm: A more agile iterative de Bruijn graph algorithm in short read genome assembly.

The de Bruijn Graph algorithm (DBG) as one of the cornerstones algorithms in short read assembly has extended with the rapid advancement of the Next Generation Sequencing (NGS) technologies and low-cost production of millions of high-quality short reads. Erroneous reads, non-uniform coverage, and genomic repeats are three major problems that influence the performance of short read assemblers. To encounter these problems, the iterative DBG algorithm applies multiple [Formula: see text]-mers instead of a single [Formula: see text]-mer, by iterating the DBG graph over a range of [Formula: see text]-mer sizes from the minimum to the maximum.

NSAMD: A new approach to discover structured contiguous substrings in sequence datasets using Next-Symbol-Array.

In many sequence data mining applications, the goal is to find frequent substrings. Some of these applications like extracting motifs in protein and DNA sequences are looking for frequently occurring approximate contiguous substrings called simple motifs. By approximate we mean that some mismatches are allowed during similarity test between substrings, and it helps to discover unknown patterns.