mutations in the gjb2 gene encoding connexin 26 (cx26) protein are a major cause for autosomal recessive non syndromic and sporadic deafness in many populations. in this study we have investigated the prevalence of the gjb2 gene mutations using nested pcr pre screening strategy and direct sequencing method. two hundred and sixty autosomal recessive non syndromic and sporadic deaf subjects from ...

prosite database contains a set of entries corresponding to protein families, which are used to identify the family of a protein from its sequence. although patterns and profiles are developed to be very selective, each may have false positive or negative hits. considering false positives as items that reduce the selectiveness of a pattern, then, the more selective pattern we have, a more accur...

Late embryogenesis abundant (LEA) proteins have been identified in a wide range of organisms and are believed to play a role in the adaptation of plants to stress conditions. In this study, we performed genome-wide identification of LEA proteins and their coding genes in Moso bamboo (Phyllostachys edulis) of Poaceae. A total of 23 genes encoding LEA proteins (PeLEAs) were found in P. edulis tha...

Residue-residue interactions that fold a protein into a unique three-dimensional structure and make it play a specific function impose structural and functional constraints in varying degrees on each residue site. Selective constraints on residue sites are recorded in amino acid orders in homologous sequences and also in the evolutionary trace of amino acid substitutions. A challenge is to extr...

A protein family contains sequences that are evolutionarily related. Generally, this is reflected by sequence similarity. There have been many attempts to organize the set of protein families into evolutionarily homogenous clusters using certain clustering methods. How do we characterize these clusters? How can we cluster protein families using these characterizations? In this work, these quest...

In protein structure space, protein structures cluster into four elongated regions when mapped based solely on similarity among the 3D structures. These four regions correspond to the four major classes of present-day proteins defined by the contents of secondary structure types and their topological arrangement. Evolution of and restriction to these four classes suggest that, in most cases, th...

The ability to build accurate protein families is a fundamental operation in bioinformatics that influences comparative analyses, genome annotation, and metabolic modeling. For several years we have been maintaining protein families for all microbial genomes in the PATRIC database (Pathosystems Resource Integration Center, patricbrc.org) in order to drive many of the comparative analysis tools ...

The ProDom database contains protein domain families generated from the SWISS-PROT database by automated sequence comparisons. It can be searched on the World Wide Web (http://protein.toulouse.inra. fr/prodom.html ) or by E-mail ([email protected]) to study domain arrangements within known families or new proteins. Strong emphasis has been put on the graphical user interface which allows ...