Motif Inference
Mostrando 1-11 de 11 artigos, teses e dissertações.
-
1. Ãndices Completos para Casamento de PadrÃes e InferÃncia de Motifs
Uma das maneiras mais eficientes (notadamente do ponto de vista computacional) empregada pela humanidade para a representaÃÃo da informaÃÃo tem sido atravÃs da forma de texto, ou seja, atravÃs de cadeias unimensionais de sÃmbolos (ou caracteres) tomados sobre conjuntos discretos finitos (ou alfabetos). As fecundas teorias, tÃcnicas e algoritmos desti
Publicado em: 2003
-
2. CisModule: De novo discovery of cis-regulatory modules by hierarchical mixture modeling
The regulatory information for a eukaryotic gene is encoded in cis-regulatory modules. The binding sites for a set of interacting transcription factors have the tendency to colocalize to the same modules. Current de novo motif discovery methods do not take advantage of this knowledge. We propose a hierarchical mixture approach to model the cis-regulatory mod
National Academy of Sciences.
-
3. Delineation of a T-cell activation motif required for binding of protein tyrosine kinases containing tandem SH2 domains.
To define the T-cell receptor signal transduction motif, we have transfected human and murine T-cell lines with a chimeric receptor consisting of the extracellular and transmembrane domains of human CD8 alpha and the membrane-proximal portion of CD3 zeta containing at its C terminus either an 18-amino acid segment (NQLYNELNLGRREEYDVL) or alanine-scanning poi
-
4. Identification of polymorphic motifs using probabilistic search algorithms
The problem of identifying motifs comprising nucleotides at a set of polymorphic DNA sites, not necessarily contiguous, arises in many human genetic problems. However, when the sites are not contiguous, no efficient algorithm exists for polymorphic motif identification. A search based on complete enumeration is computationally inefficient. We have developed
Cold Spring Harbor Laboratory Press.
-
5. Crystal structure of glycyl-tRNA synthetase from Thermus thermophilus.
The sequence and crystal structure at 2.75 A resolution of the homodimeric glycyl-tRNA synthetase from Thermus thermophilus, the first representative of the last unknown class II synthetase subgroup, have been determined. The three class II synthetase sequence motifs are present but the structure was essential for identification of motif 1, which does not po
-
6. The V(D)J recombination signal sequence and kappa B binding protein Rc binds DNA as dimers and forms multimeric structures with its DNA ligands.
The murine DNA binding protein Rc binds to the heptamer motif of the V(D)J recombination signal sequences and to the kappa B motif of the immunoglobulin enhancer. Bacterial fusion proteins for Rc and DNA ligands of Rc form multiple protein-DNA complexes in electrophoretic mobility shift assays (EMSA). Large complexes formation is favored by an increased Rc c
-
7. A 21-amino acid peptide from the cysteine cluster II of the family D DNA polymerase from Pyrococcus horikoshii stimulates its nuclease activity which is Mre11-like and prefers manganese ion as the cofactor
Family D DNA polymerase (PolD) is a new type of DNA polymerase possessing polymerization and 3′–5′ exonuclease activities. Here we report the characterization of the nuclease activity of PolD from Pyrococcus horikoshii. By site-directed mutagenesis, we verified that the putative Mre11-like nuclease domain in the small subunit (DP1), predicted according
Oxford University Press.
-
8. Single Nucleotide Polymorphism–Based Validation of Exonic Splicing Enhancers
Because deleterious alleles arising from mutation are filtered by natural selection, mutations that create such alleles will be underrepresented in the set of common genetic variation existing in a population at any given time. Here, we describe an approach based on this idea called VERIFY (variant elimination reinforces functionality), which can be used to
Public Library of Science.
-
9. Reduction of two functional gamma-globin genes to one: an evolutionary trend in New World monkeys (infraorder Platyrrhini).
Nucleotide sequences were determined for the gamma1- and gamma2-globin loci from representatives of the seven anciently separated clades in the three extant platyrrhine families (Atelidae, Pitheciidae, and Cebidae). These sequences revealed an evolutionary trend in New World monkeys either to inactivate the gamma1 gene or to fuse it with the gamma2 gene, i.e
-
10. The competence transcription factor of Bacillus subtilis recognizes short A/T-rich sequences arranged in a unique, flexible pattern along the DNA helix
The development of genetic competence in Bacillus subtilis is regulated by a complex signal transduction cascade, which leads to the synthesis of the competence transcription factor (CTF). Previous studies suggested that CTF is encoded by comK. ComK is required for the transcription of comK itself, as well as of the late competence genes encoding the DNA upt
Cold Spring Harbor Laboratory Press.
-
11. The sperm outer dense fiber protein is the 10th member of the superfamily of mammalian small stress proteins
Nine proteins have been assigned to date to the superfamily of mammalian small heat shock proteins (sHsps): Hsp27 (HspB1, Hsp25), myotonic dystrophy protein kinase–binding protein (MKBP) (HspB2), HspB3, αA-crystallin (HspB4), αB-crystallin (HspB5), Hsp20 (p20, HspB6), cardiovascular heat shock protein (cvHsp [HspB7]), Hsp22 (HspB8), and HspB9. The most p
Cell Stress Society International.