*  evolving all we are: 十月 2013
Next-Gen Sequencing Gene expression analysis shows that an AHR2 mutant fish population from the Hudson River has a dramatically ... We investigated whether there are highly conserved DNA elements without genic function in distantly related plant genomes. We ... My Weblog on Bioinformatics, Genome Science, Next Generation Sequencing Job: DATA SCIENTIST--WATSON HEALTH-CAMBRIDGE, MA. - 15 ... run gistic2 with sequenza segmentation output from whole exome sequencing - Convert sequenza output to gistic input Gistic was ...
  http://maojf.blogspot.com/2013/10/
*  Inference of Transcriptional Networks in Arabidopsis through Conserved Noncoding Sequence Analysis | Plant Cell
conserved noncoding sequence. TFBS. transcription factor binding site. CMM. Comparative Motif Mapping. FDR. false discovery ... Inference of Transcriptional Networks in Arabidopsis through Conserved Noncoding Sequence Analysis. Jan Van de Velde, Ken S. ... Inference of Transcriptional Networks in Arabidopsis through Conserved Noncoding Sequence Analysis. Jan Van de Velde, Ken S. ... Inference of Transcriptional Networks in Arabidopsis through Conserved Noncoding Sequence Analysis. Jan Van de Velde, Ken S. ...
  http://www.plantcell.org/content/26/7/2729.short
*  FuturePundit: DNA Ultra-Conserved Sequences Found Between Humans, Mice Rats
DNA Ultra-Conserved Sequences Found Between Humans, Mice Rats Comparisons between the DNA sequences of humans, mice, rats, and ... The first indication of the existence of ultra-conserved sequence regions was found in the initial comparison of the human and ... Researchers have found precisely the same sequences in the genomes of humans, rats, and mice; sequences that are 95 to 99 ... Comparison between the genomes of humans, mice, and rats showed many identical sequences. Most of those sequences do not code ...
  http://www.futurepundit.com/archives/002095.html
*  RNase T shares conserved sequence motifs with DNA proofreading exonucleases.
... E V Koonin and M P Deutscher ... Sequence analysis of the Escherichia coli dnaE gene. J Bacteriol. 1987 Dec;169(12):5735-5744. [PMC free article] [PubMed] ... Sequence and transcriptional analysis of the Escherichia coli rnt gene encoding RNase T. J Biol Chem. 1992 Dec 15;267(35):25609 ...
  http://pubmedcentralcanada.ca/pmcc/articles/PMC309564/?lang=en-ca
*  Conserved sequence - Wikipedia
Identifying conserved sequences can be used to discover and predict functional sequences such as genes. Conserved sequences ... Sequences may also recombine or be deleted due to chromosomal rearrangements. Conserved sequences are sequences which persist ... Highly conserved DNA sequences are thought to have functional value, although the role for many highly conserved non-coding DNA ... In evolutionary biology, conserved sequences are similar or identical sequences in nucleic acids (DNA and RNA) or proteins ...
  https://en.wikipedia.org/wiki/Conserved_sequence
*  WebLogo displaying conserved sequences associated with | Open-i
WebLogo displaying conserved sequences associated with frameshift sites.Sizes of letters denote information content, or ... To search the potential conserved sequence elements, 30 bp upstream and downstream of the conserved slippery sequence motif ... To search the potential conserved sequence elements, 30 bp upstream and downstream of the conserved slippery sequence motif ... Consistent with a previous report, no conserved sequence element was found except the slippery site sequence 5′-WWW TAR-3′ (W=A ...
  https://openi.nlm.nih.gov/detailedresult.php?img=PMC4759687_srep21139-f4&req=4
*  "Structure-function studies of conserved sequence motifs of cytochrome " by Louis J. Crowley
Within these domains are highly conserved 'motifs' necessary for the proper binding and orientation of both the NADH coenzyme ... To address the importance of these conserved motifs site-directed mutagenesis was utilized to generate a series of variants ... The role of the '124GRxxST127' was determined by the introduction of a positive charge, charge reversal, and conserved amino ... mutants that are found within or in close proximity to these highly conserved motifs were analyzed utilizing site-directed ...
  http://scholarcommons.usf.edu/etd/682/
*  Mutagenesis of charged residues in a conserved sequence in the 2-kinase domain of 6-phosphofructo-2-kinase/fructose-2,6...
Mutagenesis of charged residues in a conserved sequence in the 2-kinase domain of 6-phosphofructo-2-kinase/fructose-2,6- ... Mutagenesis of charged residues in a conserved sequence in the 2-kinase domain of 6-phosphofructo-2-kinase/fructose-2,6- ... Mutagenesis of charged residues in a conserved sequence in the 2-kinase domain of 6-phosphofructo-2-kinase/fructose-2,6- ... Mutagenesis of charged residues in a conserved sequence in the 2-kinase domain of 6-phosphofructo-2-kinase/fructose-2,6- ...
  http://www.biochemj.org/content/323/3/863.3
*  Disease-associated variants in PYPAF1 and NOD2 result in similar alterations of conserved sequence. | IKMB
Disease-associated variants in PYPAF1 and NOD2 result in similar alterations of conserved sequence. Institut für Klinische ... Disease-associated variants in PYPAF1 and NOD2 result in similar alterations of conserved sequence. ... A multiple sequence alignment of homologous proteins demonstrates that some of the missense variants are located in highly ... Sequence variations in the gene products PYPAF1/CIAS1 and NOD2/CARD15 have been associated with several autoinflammatory ...
  http://www.ikmb.uni-kiel.de/publications/disease-associated-variants-pypaf1-and-nod2-result-similar-alterations-conserved
*  Specific and conserved sequences in D. melanogaster and C. elegans lamins and histone H2A mediate the attachment of lamins to...
Specific and conserved sequences in D. melanogaster and C. elegans lamins and histone H2A mediate the attachment of lamins to ... The evolutionarily conserved NLS motif and T/SRAT/S sequence probably play a role in the binding of other lamins to chromatin ... Specific and conserved sequences in D. melanogaster and C. elegans lamins and histone H2A mediate the attachment of lamins to ... Specific and conserved sequences in D. melanogaster and C. elegans lamins and histone H2A mediate the attachment of lamins to ...
  http://jcs.biologists.org/content/120/1/77
*  RCSB PDB - 141D: SOLUTION STRUCTURE OF A CONSERVED DNA SEQUENCE FROM THE HIV-1 GENOME: RESTRAINED MOLECULAR DYNAMICS...
Solution structure of a conserved DNA sequence from the HIV-1 genome: restrained molecular dynamics simulation with distance ... SOLUTION STRUCTURE OF A CONSERVED DNA SEQUENCE FROM THE HIV-1 GENOME: RESTRAINED MOLECULAR DYNAMICS SIMULATION WITH DISTANCE ...
  http://www.rcsb.org/pdb/explore/materialsAndMethods.do?structureId=141D
*  A short peptide sequence is conserved between three tick-borne Borrelia | Biochemical Society Transactions
A short peptide sequence is conserved between three tick-borne Borrelia. LYN HAYES, LEONARD C. ARCHARD, DAVID J. M. WRIGHT ... A short peptide sequence is conserved between three tick-borne Borrelia Message Subject (Your Name) has forwarded a page to you ...
  http://www.biochemsoctrans.org/content/15/4/644.1
*  Refining multiple sequence alignments with conserved core regions
... Saikat Chakrabarti, Christopher J. Lanczycki, Anna R. ... A block model represents conserved sequence/structure regions which are highly unlikely to contain gaps and are common to all ... Realignment of each sequence can correct misalignments between a given sequence and the rest of the profile and at the same ... Realignment of each sequence can correct misalignments between a given sequence and the rest of the profile by shifting the ...
  http://pubmedcentralcanada.ca/pmcc/articles/PMC1463900/?lang=en-ca
*  Improving protein structure similarity searches using domain boundaries based on conserved sequence information | BMC...
... we have investigated how alternative definitions of domains derived from conserved sequence alignments in the Conserved Domain ... A sequence-based domain can generally be defined as an evolutionarily conserved region of a protein. Domains of this type are ... Identifying sequence domains disagreeing with structure domains. The April 2005 Conserved Domain Database (CDD) and medium ... Structure DomainSequence DomainConserve Domain DatabaseCatalytic Core DomainDomain Difference ...
  https://bmcstructbiol.biomedcentral.com/articles/10.1186/1472-6807-9-33
*  A single amino acid substitution (N297A) in the conserved NPXXY sequence of the human N-formyl peptide receptor results in...
A single amino acid substitution (N297A) in the conserved NPXXY sequence of the human N-formyl peptide receptor results in ... A single amino acid substitution (N297A) in the conserved NPXXY sequence of the human N-formyl peptide receptor results in ... A single amino acid substitution (N297A) in the conserved NPXXY sequence of the human N-formyl peptide receptor results in ... A single amino acid substitution (N297A) in the conserved NPXXY sequence of the human N-formyl peptide receptor results in ...
  http://www.biochemj.org/content/352/2/399
*  Conserved non-coding sequence - Wikipedia
A conserved non-coding sequence (CNS) is a DNA sequence of noncoding DNA that is evolutionarily conserved. These sequences are ... Conserved non-coding sequences can be important sites of evolutionary divergence as mutations in these regions may alter the ... Jan 2005). "Plant conserved non-coding sequences and paralogue evolution". Trends in Genetics. 21 (1): 60-65. doi:10.1016/j.tig ... Intron sequences may be conserved, often because they contain expression regulating elements that put functional constraints on ...
  https://en.wikipedia.org/wiki/Conserved_non-coding_sequence
*  Frontiers | Control regions for chromosome replication are conserved with respect to sequence and location among Escherichia...
The structural organization of oriC, datA, DARS1 and DARS2 were found conserved between 59 fully sequenced E. coli genomes, ... The structural organization of oriC, datA, DARS1 and DARS2 were found conserved between 59 fully sequenced E. coli genomes, ... The relative distances from oriC to datA, DARS1 and DARS2, respectively, was also conserved despite of large variations in ... We suggest that this fitness cost contribute to conservation of both sequence and chromosomal location for datA, DARS1 and ...
  https://www.frontiersin.org/articles/10.3389/fmicb.2015.01011/full
*  The Highly Conserved Codon following the Slippery Sequence Supports −1 Frameshift Efficiency at the HIV-1 Frameshift Site
A slippery sequence, U UUU UUA, and a stem-loop are well-defined RNA features modulating −1 frameshifting in HIV-1. The GGG ... This GGG codon is highly conserved in natural isolates of HIV. When the natural intercodon was replaced with a stop codon two ... glycine codon immediately following the slippery sequence (the 'intercodon') contributes structurally to the start of the stem- ...
  http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0122176
*  A highly conserved G-rich consensus sequence in hepatitis C virus core gene represents a new anti-hepatitis C target | Science...
A highly conserved G-rich consensus sequence in hepatitis C virus core gene represents a new anti-hepatitis C target ... A highly conserved G-rich consensus sequence in hepatitis C virus core gene represents a new anti-hepatitis C target ... A highly conserved G-rich consensus sequence in hepatitis C virus core gene represents a new anti-hepatitis C target ... A highly conserved G-rich consensus sequence in hepatitis C virus core gene represents a new anti-hepatitis C target ...
  http://advances.sciencemag.org/content/2/4/e1501535
*  Abstract 2926: Histologically defined intratumoral sequencing uncovers evolutionary cues into conserved molecular events...
Histologically defined intratumoral sequencing uncovers evolutionary cues into conserved molecular events driving gliomagenesis ... Abstract 2926: Histologically defined intratumoral sequencing uncovers evolutionary cues into conserved molecular events ... Abstract 2926: Histologically defined intratumoral sequencing uncovers evolutionary cues into conserved molecular events ... Abstract 2926: Histologically defined intratumoral sequencing uncovers evolutionary cues into conserved molecular events ...
  http://cancerres.aacrjournals.org/content/77/13_Supplement/2926
*  Analysis of conserved binding proteins for nuclear localization sequences | Journal of Cell Science
Analysis of conserved binding proteins for nuclear localization sequences. U. Stochaj, M.A. Bossie, K. van Zee, A.M. Whalen, P. ... Analysis of conserved binding proteins for nuclear localization sequences. U. Stochaj, M.A. Bossie, K. van Zee, A.M. Whalen, P. ... Analysis of conserved binding proteins for nuclear localization sequences. U. Stochaj, M.A. Bossie, K. van Zee, A.M. Whalen, P. ... Analysis of conserved binding proteins for nuclear localization sequences Message Subject (Your Name) has sent you a message ...
  http://jcs.biologists.org/content/104/1/89
*  Sequence Similarity - 1I36: Structure of Conserved Protein MTH1747 of Unknown Function Reveals Structural Similarity...
Sequence Similarity Clusters for the Entities in PDB 1I36 Legend Entity #1 , Chains: A,B CONSERVED HYPOTHETICAL PROTEIN MTH1747 ... Structures of protein chains with identical sequences (sequence identity > 95%) are aligned, superimposed and clustered. ... Blast this sequence against all of PDB Archive.. Rank. In each cluster, the chains are sorted (i.e. ranked) according to the ... Sequence Similarity Cutoff. Rank. Chains in Cluster. Cluster ID / Name. Structural variation in cluster. ...
  http://www.rcsb.org/pdb/explore/sequenceCluster.do?structureId=1I36
*  Algorithms currently supported by the Sockeye Platform (through Chinook) - Canada's Michael Smith Genome Sciences Centre
Multi-species Conserved Sequences. MCS Analysis E.H. Margulies, M. Blanchette, NISC Comparative Sequencing Program, D. Haussler ... CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific ... and E.D. Green "Identification and Characterization of Multi-Species Conserved Sequences" Genome Research (13:2507-2518) Primer ... Regulatory sequence analysis tools. Nucleic Acids Res 31: 3593-3596. (*)STUBB Sinha, S., E. Van Nimwegen, and E.D. Siggia. 2003 ...
  http://www.bcgsc.ca/project/bomge/sockeye/algorithms
*  Structure Cluster - 1JTN: Alternative Structures of a Sequence Extended T4 Lysozyme Show that the Highly Conserved...
Demonstrate that the Highly Conserved beta-Sheet Region has Low Intrinsic Folding Propensity ... Alternative Structures of a Sequence Extended T4 Lysozyme Show that the Highly Conserved Beta-Sheet Region has weak intrinsic ... ID: % sequence identity in the alignment. A 40% sequence identity filter is applied before the structure alignments are ... If the sequences are of vastly different lengths, the clustering procedure will group them in different clusters, even if they ...
  http://www.rcsb.org/pdb/explore/structureCluster.do?structureId=1JTN