an important step in considering of gene expression data is obtained groups of genes that have similarity patterns. biclustering methods was recently introduced for discovering subsets of genes that have coherent values across a subset of conditions. the las algorithm relies on a heuristic randomized search to find biclusters. in this paper, we introduce biclustering las algorithm and then appl...

Sequence alignment in bioinformatics is a field of research focused on developing tools for comparing and finding similar sequences of amino acids or DNA base pairs with the aid of computers. The sequence similarity is used to assess gene and protein homology, classify genes and proteins, predict biological function, secondary and tertiary protein structure, detect point mutations, construct ev...

The intestinal bacterial diversity of Stichopus japonicus was investigated using 16S ribosomal RNA gene (rDNA) clone library and Polymerase Chain Reaction/Denaturing Gradient Gel Electrophoresis (PCR-DGGE). The clone library yielded a total of 188 clones, and these were sequenced and classified into 106 operational taxonomic units (OTUs) with sequence similarity ranging from 88 to 100%. The cov...

The great majority of biological sequences share significant similarity with other sequences as a result of evolutionary processes, and identifying these sequence similarities is one of the most challenging problems in bioinformatics. In this paper, we present a discrete artificial bee colony (ABC) algorithm, which is inspired by the intelligent foraging behavior of real honey bees, for the det...

The combination of sequencing and post-sequencing experimental approaches produces huge collections of data that are highly heterogeneous both in structure and in semantics. We propose a new strategy for the integration of such data. This strategy uses structured sets of sequences as a unified representation of biological information and defines a probabilistic measure of similarity between the...

We have designed and implemented a software package for the automatic high-throughput function prediction for genes. This system attempts to assign a biological function to protein sequences by carrying out searches in sequence databanks and by locating functionally relevant motifs in the query sequences. The results produced by the various prediction methods consist of the annotations of match...

Biological sequence comparison is one of the most important tasks in Bioinformatics. Due to the growth of biological databases, sequence comparison is becoming an important challenge for high performance computing, especially when very long sequences are compared. The Smith-Waterman (SW) algorithm is an exact method based on dynamic programming to quantify local similarity between sequences. Th...