نتایج جستجو برای: consensus sequence

تعداد نتایج: 478416  

Journal: :Computer applications in the biosciences : CABIOS 1990
G. Z. Hertz G. W. Hartzell Gary D. Stormo

We have developed a method for identifying consensus patterns in a set of unaligned DNA sequences known to bind a common protein or to have some other common biochemical function. The method is based on a matrix representation of binding site patterns. Each row of the matrix represents one of the four possible bases, each column represents one of the positions of the binding site and each eleme...

Journal: :PLoS Computational Biology 2008
Ignacio E. Sánchez Pedro Beltrão François Stricher Joost Schymkowitz Jesper Ferkinghoff-Borg Frederic Rousseau Luis Serrano

Current experiments likely cover only a fraction of all protein-protein interactions. Here, we developed a method to predict SH2-mediated protein-protein interactions using the structure of SH2-phosphopeptide complexes and the FoldX algorithm. We show that our approach performs similarly to experimentally derived consensus sequences and substitution matrices at predicting known in vitro and in ...

2008
Christina Boucher Daniel G. Brown Stephane Durocher

Abstract. Given a set of sequences, S, and degeneracy parameter, d, the Consensus Sequence problem asks whether there exists a sequence that has Hamming distance at most d from each sequence in S. A valid motif set is a set of sequences for which such a consensus sequence exists, while a decoy set is a set of sequences that does not have a consensus sequence but whose pairwise Hamming distances...

Journal: :iranian journal of parasitology 0
shirzad gholami hefzallah jahandar mahdi abastabar abdolsatar pagheh iraj mobedi mitra sharbatkhori

background : the aim of the present study was genotyping of echinococcus granulosus isolates from dogs and jackals in mazandaran province, northern iran, and using partial sequence of the mitochondrial cytochrome c oxidase subunit 1 gene ( cox1 ). methods: e. granulosus isolates (n = 15) were collected from 42 stray dogs and 16 jackals found in south of the caspian sea in northern iran. after m...

2003
Conrad Shyu James A. Foster

In this paper we present an approach that employs a genetic algorithm (GA) to evolve the consensus sequences for DNA and protein sequences alignments. We have developed an encoding scheme such that the number of generations needed to find the optimal solution remains approximately the same regardless the number of sequences. The complexity instead depends only on the length of the consensus seq...

1999
Stefanie N. Vogel Teri Sullivan Keiko Ozato Matthew J. Fenton Wannee Kantakamalakul Alexander D. Politis Sylvia Marecki

Journal: :Nucleic acids research 1997
N Tolstrup P Rouzé S Brunak

Little knowledge exists about branch points in plants; it has even been claimed that plant introns lack conserved branch point sequences similar to those found in vertebrate introns. A putative branch point consensus sequence for Arabidopsis thaliana resembling the well known metazoan consensus sequence has been proposed, but this is based on search of sequences similar to those in yeast and me...

2008
Alberto Sola-Landa Antonio Rodríguez-García Alexander Kristian Apel Juan F. Martín

Expression of genes belonging to the pho regulon in Streptomyces coelicolor is positively regulated (as shown by comparing the wild-type and a DeltaphoP mutant) by binding of the response regulator PhoP to 11-nt direct repeats (DRus). These sequences have been found in over 100 genes of Streptomyces coelicolor; 20 of them were cloned and the binding of PhoP(DBD) to most of their promoters has b...

Journal: :Chemical communications 2016
Y Sun L M Willis H R Batchelder M Nitz

Using a MALDI-MS based assay, the kinetic parameters for peptide glucosylation using the C. difficile toxin B glycosyltransferase domain were determined. The minimum consensus sequence for glucosylation was YXXTXFXXY and the optimal peptide found was YAPTVFDAY. Using this sequence, homogenous glucosylated proteins could be readily produced.

Journal: :Proceedings of the National Academy of Sciences of the United States of America 2002
Jonathan H Davis Jack W Szostak

Aptamers, RNA sequences that bind to target ligands, are typically isolated by in vitro selection from RNA libraries containing completely random sequences. To see whether higher-affinity aptamers can be isolated from partially structured RNA libraries, we selected for aptamers that bind GTP, starting from a mixture of fully random and partially structured libraries. Because stem-loops are comm...

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