The goal of this paper is to propose the performance evaluation of the scaling of parallel software for biological sequence alignment and homology searching based on blast algorithm for sequence searching and clustalw algorithm for multiple sequence alignment on the supercomputer BlueGene/P for the case study of influenza virus sequences variability and homology searching with human genome.

Methods for collecting related segments from the protein sequence database using strongly conserved peptide words as well as sequence homology was applied to the problem of reconstruction of PROSITE catalog [1] from the sequence database. In many case our results were well consistent with PROSITE although some additional relationships were also found.

Section 2. Then we present ProtoNet. ProtoNet is centered around the concept of homology transitivity. ProtoNet clusters protein sequences into a hierarchy based on sequence similarity and homology transitivity. Thus the hierarchy parallels the evolutionary history of these protein sequences. We then illustrate—using Histone proteins—the application of ProtoNet to detect remote protein relatives.

Alignments of frequency profiles against frequency profiles have a wide scope of applications in currently used bioinformatic analysis tools ranging from multiple alignment methods based on the progressive alignment approach to detecting of structural similarities based on remote sequence homology. We present the new log average scoring approach to calculating the score to be used with alignmen...

Different procedures for obtaining homology models for P450s are investigated using various sequence alignments sharing various levels of sequence identity with available P450 crystal structures. In this analysis, we have investigated how well homology modeling can reproduce known crystal structures as well as how effectively these homology models can be used to reproduce known ligand-binding m...

Background: Coccidiosis caused by Eimeria necatrix has the most economic impact onpoultry production. Micronemal proteins in Eimeria necatrix are thoughtto be critical ligands determining host cell specificity at the time ofinvasion.               OBJECTIVES: Isolation and purification of Eimeria necatrix oocysts from  Khuzestan province of Iran was performed. AcDNA encoding microneme 5 (EnMIC5...

In [28], Lawrence Roberts, extending the work of Ozsváth and Szabó in [23], showed how to associate to a link, L, in the complement of a fixed unknot, B ⊂ S, a spectral sequence whose E term is the Khovanov homology of a link in a thickened annulus defined in [2], and whose E term is the knot Floer homology of the preimage of B inside the double-branched cover of L. In [6], we extended [23] in ...

Extensive amino acid sequence homology has been found between nine tryptic peptides of pig heart lipoamide dehydrogenase (NADH:lipoamide oxidoreductase, EC 1.6.4.3] and the sequence of human erythrocyte glutathione reductase [NAD(P)H:glutathione oxidoreductase, EC 1.6.4.2]. The average homology is 40%. Six lipoamide dehydrogenase peptides are homologous with segments of the two parts of the FAD...

Several repetitive sequence elements from diverse species share extensive sequence homology with tRNA molecules. Analysis of the tRNA-like sequences within these elements suggest that they have originated from authentic tRNA sequences. Elements containing tRNA-like sequences can be divided into three distinct groups whose members share extensive sequence homology, have similar sequence organiza...

The most important in silico methods, to exploit the amount of new genomic data, are based on the concept of homology. The principle of homology-based analysis is to identify a homology relationship between a new protein and a protein whose function is known. For remote homologs, sequence alignment methods fail. In such a case one aligns the sequence of a new protein with the 3D structures of k...