Local Sequence Algignment. The local sequence alignment problem is defined as follows: Given two strings S = s 1. .. s n and T = t 1. .. t m , a substitution matrix Score and an insertion/deletion penalty δ, find a pair of substrings s i. .. s i+k of S and t j. .. t j+l of T that have the best overall alignment score, and return the best alignment for them. Local Sequence Algignment against a d...

Finding regions of similarity between two very long data streams is a computationally intensive problem referred to as sequence alignment. Alignment algorithms must allow for imperfect sequence matching with different starting locations and some gaps and errors between the two data sequences. Perhaps the most well known application of sequence matching is the testing of DNA or protein sequences...

The Smith-Waterman algorithm for local sequence alignment is one of the most important techniques in computational molecular biology. This ingenious dynamic programming approach was designed to reveal the highly conserved fragments by discarding poorly conserved initial and terminal segments. However, the existing notion of local similarity has a serious aw: it does not discard poorly conserved...

Naturally occurring polarized light is used for orientation by many arthropods. Various insects and chelicerates as well as crustaceans, employing either their simple or compound eyes, can detect the pattern of linearly polarized light in the blue sky and from it determine geographical direction. Among Crustacea, the semi-terrestrial beach amphipod TaUtrus and the isopod Tylos show this when, o...

MOTIVATION Sequence database searching is among the most important and challenging tasks in bioinformatics. The ultimate choice of sequence-search algorithm is that of Smith-Waterman. However, because of the computationally demanding nature of this method, heuristic programs or special-purpose hardware alternatives have been developed. Increased speed has been obtained at the cost of reduced se...

Since the discovery of RNA Interference (RNAi), a cellular phenomenon in which a small double stranded RNA induces the degradation of its sequence specific target mRNA, using a computer-aided software tool to help design functional small interfering RNA (siRNA) or small hairpin RNA (shRNA) has become a standard procedure in applying RNAi to silence a target gene. A critical consideration in siR...

Genomic sequence alignment is an important technique to decode genome sequences in bioinformatics. Next-Generation Sequencing technologies produce genomic data of longer reads. Cloud platforms are adopted to address the problems arising from storage and analysis of large genomic data. Existing genes sequencing tools for cloud platforms predominantly consider short read gene sequences and adopt ...