background: escherichia coli is a commensal-pathogenic organism, which includes a wide range of strains. despite several advanced molecular-genomic technologies for detecting and identifying different strains of e. coli, enterobacterial repetitive intergenic consensus polymerase chain reaction (eric-pcr) technique is a quick, sharp and cost effective fingerprint method. the major purpose of the...

The evolution of molecular quasispecies on two diierent complex tness landscapes, the Sherrington Kirkpatrick spin glass and the Graph Bipartitioning landscape, is investigated in dependence on replication delity and population size. Three diierent regimes of replication delity are detected. At high copying delity one obtains a population with high mean tness localized around a time independent...

We have developed a novel representation of protein motifs that permits the rapid discovery of structural features in sets of protein sequences with a common structure or function. Many popular methods for representing protein motifs (consensus sequences, weight matrices, profiles, etc.) emphasize conservation of amino acids at specific sites in the sequence. Our method looks for correlations b...

We analyzed a total of 27,958,007 sequences that all had perfect matches to the expected indices (Extended Data Table 6). We merged the reads from either end of the same molecule by requiring an overlap of at least 11 base pairs, and generated a consensus sequence by picking the base with the higher sequence quality. We mapped these merged reads, which we call a “fragment”, to the revised Cambr...

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Minimotif Miner (MnM available at http://minimotifminer.org or http://mnm.engr.uconn.edu) is an online database for identifying new minimotifs in protein queries. Minimotifs are short contiguous peptide sequences that have a known function in at least one protein. Here we report the third release of the MnM database which has now grown 60-fold to approximately 300,000 minimotifs. Since short mi...

Consensus sequences are widely used in molecular biology but they have many flaws. As a result, binding sites of proteins and other molecules are missed during studies of genetic sequences and important biological effects cannot be seen. Information theory provides a mathematically robust way to avoid consensus sequences. Instead of using consensus sequences, sequence conservation can be quanti...

Objective(s): Production of a recombinant and immunogenic antigen using dengue virus type-3 envelope protein is a key point in dengue vaccine development and diagnostic researches. The goals of this study were providing a recombinant protein from dengue virus type-3 envelope protein and evaluation of its immunogenicity in mice. Materials and Methods: Multiple amino acid sequences of different i...