Families Of Matrices
Mostrando 13-24 de 25 artigos, teses e dissertações.
-
13. Panning for Genes—A Visual Strategy for Identifying Novel Gene Orthologs and Paralogs
We have developed a rapid visual method for identifying novel members of gene families. Starting with an evolutionary tree, 20–50 protein query sequences for a gene family are selected from different branches of the tree. These query sequences are used to search the GenBank and expressed sequence tag (EST) DNA databases and their nightly updates using the
Cold Spring Harbor Laboratory Press.
-
14. GFScan: A Gene Family Search Tool at Genomic DNA Level
We have developed GFScan (Gene Family Scan), a tool that identifies members of a gene family by searching genomic DNA sequences with genomic DNA motifs (or matrices) that are representative of the family. We have tested GFScan on four human gene families including the neurotransmitter-gated ion-channels (NGIC) family, the carbonic anhydrases (CA) family, the
Cold Spring Harbor Laboratory Press.
-
15. Local feature frequency profile: A method to measure structural similarity in proteins
Measures of structural similarity between known protein structures provide an objective basis for classifying protein folds and for revealing a global view of the protein structure universe. Here, we describe a rapid method to measure structural similarity based on the profiles of representative local features of Cα distance matrices of compared protein str
National Academy of Sciences.
-
16. Large-scale temporal gene expression mapping of central nervous system development
We used reverse transcription–coupled PCR to produce a high-resolution temporal map of fluctuations in mRNA expression of 112 genes during rat central nervous system development, focusing on the cervical spinal cord. The data provide a temporal gene expression “fingerprint” of spinal cord development based on major families of inter- and intracellular
National Academy of Sciences.
-
17. AthaMap: an online resource for in silico transcription factor binding sites in the Arabidopsis thaliana genome
Gene expression is controlled mainly by the binding of transcription factors to regulatory sequences. To generate a genomic map for regulatory sequences, the Arabidopsis thaliana genome was screened for putative transcription factor binding sites. Using publicly available data from the TRANSFAC database and from publications, alignment matrices for 23 transc
Oxford University Press.
-
18. Recent enhancements to the Blocks Database servers.
The Blocks Database contains multiple alignments of conserved regions in protein families which can be searched by e-mail ([email protected]) and World Wide Web (http://blocks.fhcrc.org/ ) servers to classify protein and nucleotide sequences. Recent enhancements to the servers include: (i) improved calculation of position-specific scoring matrices from
-
19. SURVEY AND SUMMARY: The non-Watson–Crick base pairs and their associated isostericity matrices
RNA molecules exhibit complex structures in which a large fraction of the bases engage in non-Watson–Crick base pairing, forming motifs that mediate long-range RNA–RNA interactions and create binding sites for proteins and small molecule ligands. The rapidly growing number of three-dimensional RNA structures at atomic resolution requires that databases c
Oxford University Press.
-
20. Identification of New Herpesvirus Gene Homologs in the Human Genome
Viruses are intracellular parasites that use many cellular pathways during their replication. Large DNA viruses, such as herpesviruses, have captured a repertoire of cellular genes to block or mimic host immune responses, apoptosis regulation, and cell-cycle control mechanisms. We have conducted a systematic search for all homologs of herpesvirus proteins in
Cold Spring Harbor Laboratory Press.
-
21. eBLOCKs: enumerating conserved protein blocks to achieve maximal sensitivity and specificity
Classifying proteins into families and superfamilies allows identification of functionally important conserved domains. The motifs and scoring matrices derived from such conserved regions provide computational tools that recognize similar patterns in novel sequences, and thus enable the prediction of protein function for genomes. The eBLOCKs database enumera
Oxford University Press.
-
22. Superior performance in protein homology detection with the Blocks Database servers.
The Blocks Database World Wide Web (http://www.blocks.fhcrc.org ) and Email ([email protected]) servers provide tools for the detection and analysis of protein homology based on alignment blocks representing conserved regions of proteins. During the past year, searching has been augmented by supplementation of the Blocks Database with blocks from the P
-
23. Genetic, geographic, and linguistic distances in Europe.
Genetic and taxonomic distances were computed for 3466 samples of human populations in Europe based on 97 allele frequencies and 10 cranial variables. Since the actual samples employed differed among the genetic systems studied, the genetic distances were computed separately for each system, as were matrices of geographic distances and of linguistic distance
-
24. Scansite 2.0: proteome-wide prediction of cell signaling interactions using short sequence motifs
Scansite identifies short protein sequence motifs that are recognized by modular signaling domains, phosphorylated by protein Ser/Thr- or Tyr-kinases or mediate specific interactions with protein or phospholipid ligands. Each sequence motif is represented as a position-specific scoring matrix (PSSM) based on results from oriented peptide library and phage di
Oxford University Press.