The comparison of one nucleotide or amino-acid sequence with another to find the degree of similarity between them is a key technique in present-day biology. A marked similarity between two gene or protein sequences may reflect the fact that they are derived by evolution from the same ancestral sequence. Sequences related in this way are called homologous and the evolutionary similarity between...

Protein function assignments based on postulated homology as recognized by high sequence similarity are used routinely in genome analysis. Improvements in sensitivity of sequence comparison algorithms got to the point, that proteins with previously undetectable sequence similarity, such as for instance 10-15% of identical residues, sometimes can be classified as similar. What is the relation be...

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...

We introduce a geometric framework suitable for studying the relationships among biological sequences. In contrast to previous works, our formulation allows asymmetric distances (quasi-metrics), originating from uneven weighting of strings, which may induce non-trivial partial orders on sets of biosequences. The distances considered are more general than traditional generalized string edit dist...

We present in this paper a peptide matching approach to the multiple comparison of a set of protein sequences. This approach consists in looking for all the words that are common to q of these sequences, where q is a parameter. The comparison between words is done by using as reference an object called a model. In the case of proteins, a model is a product of subsets of the alphabet Σ of the am...

Pair-wise sequence alignment is the basic method of comparative analysis of proteins and nucleic acids. Studying the results of the alignment one has to consider two questions: (1) did the program find all the interesting similarities (“sensitivity”) and (2) are all the found similarities interesting (“selectivity”). Definitely, one has to specify, what alignments are considered as the interest...

MOTIVATION SAMBA (Systolic Accelerator for Molecular Biological Applications) is a 128 processor hardware accelerator for speeding up the sequence comparison process. The short-term objective is to provide a low-cost board to boost PC or workstation performance on this class of applications. This paper places SAMBA amongst other existing systems and highlights the original features. RESULTS R...

Modern sequence alignment algorithms are used routinely to identify homologous proteins, proteins that share a common ancestor. Homologous proteins always share similar structures and often have similar functions. Over the past 20 years, sequence comparison has become both more sensitive, largely because of profile-based methods, and more reliable, because of more accurate statistical estimates...

Let A and B be two sequences of length M and N respectively, where without loss of generality N ≥ M, and let D be the length of a shortest edit script between them. A parameter related to D is the number of deletions in such a script, P = D/2 − (N − M)/2. We present an algorithm for finding a shortest edit distance of A and B whose worst case running time is O(NP) and whose expected running tim...

We surveyed several important formulations of the sequence database search problem (i.e. local sequence alignment) as well as their solutions. These include the Maximal Segment Pair (MSP) formulation, which has a trivial dynamic programming solution and serve as the basis for popular heuristic solutions such as BLAST 2] and FASTA 18]. The local alignment with gaps formulation as well as a restr...