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ProfileGrids as a new visual representation of large multiple sequence alignments: a case study of the RecA protein family

By Alberto I Roca, Albert E Almada and Aaron C Abajian
Topics: Software
Publisher: BioMed Central
OAI identifier: oai:pubmedcentral.nih.gov:2663765
Provided by: PubMed Central

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Citations

  1. (1998). A: Specific RecA amino acid changes affect RecA-UmuD'C interaction. Mol Microbiol
  2. (1990). A: The P-loop: a common motif in ATP- and GTP-binding proteins. Trends Biochem Sci
  3. (2001). AJ: Analysis of a data set of paired uncomplexed protein structures: new metrics for side-chain flexibility and model evaluation. Proteins
  4. (2008). Alonso JC: Bacillus subtilis SsbA and dATP regulate RecA nucleation onto single-stranded DNA. DNA Repair
  5. (1993). ALSCRIPT: a tool to format multiple sequence alignments. Protein Eng
  6. (1974). Amino acid difference formula to help explain protein evolution. Science
  7. (2005). Apweiler R: The EMBL Nucleotide Sequence Database. Nucleic Acids Res
  8. (1991). Attwood TK: SOMAP: a novel interactive approach to multiple protein sequences alignment. Comput Appl Biosci
  9. (1995). Bacterial classifications derived from RecA protein sequence comparisons.
  10. BCH: JColorGrid: software for the visualization of biological measurements.
  11. (2001). BG: Complete genome sequence of a multiple drug resistant Salmonella enterica serovar Typhi CT18. Nature
  12. (2006). Biocurators: contributors to the world of science.
  13. (2000). Bioinformatics: Converting Data to Knowledge: A Workshop Summary
  14. (2000). Bleasby A: EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet
  15. (1999). Camerini-Otero RD: Saturation mutagenesis of the E. coli RecA loop L2 homologous DNA pairing region reveals residues essential for recombination and recombinational repair.
  16. (2005). Comparative and evolutionary analysis of the bacterial homologous recombination systems. PLoS Genet
  17. (1974). Concepts and Approaches in Animal Morphology Assen, The Netherlands: Van Gorcum & Comp;
  18. (1983). Correlation of sequence hydrophobicities measures similarity in three-dimensional protein structure.
  19. (2006). Cox MM: Complementation of one RecA protein point mutation by another. Evidence for trans catalysis of ATP hydrolysis.
  20. (1997). Cox MM: RecA protein: structure, function, and role in recombinational DNA repair. Prog Nucleic Acid Res Mol Biol
  21. (1997). DG: The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res
  22. (1990). DNA sequence analysis of the recA genes from Proteus vulgaris,
  23. (2000). DNASTAR's Lasergene sequence analysis software. Methods Mol Biol
  24. (2004). Environmental genome shotgun sequencing of the Sargasso Sea. Science
  25. (1999). FR: Reevaluation of the nucleotide cofactor specificity of the RecA protein from Bacillus subtilis.
  26. (2004). GJ: The Jalview Java alignment editor. Bioinformatics
  27. (2005). Gojobori T: DDBJ in collaboration with mass-sequencing teams on annotation. Nucleic Acids Res
  28. (2000). Ikemura T: Codon usage tabulated from international DNA sequence databases: status for the year 2000. Nucleic Acids Res
  29. (1997). Initial characterization of mutants in a universally conserved RecA structural motif.
  30. (1997). Insights into thermal resistance of proteins from the intrinsic stability of their alpha-helices. Proteins
  31. instructions: Sequence alignments [ h t t p : /
  32. (2000). Inteins invading mycobacterial RecA proteins. FEBS Lett
  33. (1965). Isolation and characterization of recombination-deficient mutants of Escherichia coli K-12. Proc Natl Acad Sci USA
  34. (2000). Kanehisa M: AAindex: amino acid index database.
  35. (2003). Knight KL: Molecular design and functional organization of the RecA protein. Crit Rev Biochem Mol Biol
  36. (1990). Kokjohn TA: General microbiology of recA: environmental and evolutionary significance. Annu Rev Microbiol
  37. (1993). Kowalczykowski SC: Negative co-dominant inhibition of RecA protein function: biochemical properties of the RecA1, RecA13 and RecA56 proteins and the effect of RecA56 protein on the activities of the wild-type RecA protein function in vitro.
  38. (1996). Kowalczykowski SC: The DNA binding site(s) of the Escherichia coli RecA protein.
  39. (1990). Lipman DJ: Basic local alignment search tool.
  40. (2005). LS: The Universal Protein Resource (UniProt). Nucleic Acids Res
  41. (1978). Matrices for detecting distant relationships.
  42. (2008). MM: Defective dissociation of a "slow" RecA mutant protein imparts an Escherichia coli growth defect.
  43. (1995). MM: The deduced Vibrio cholerae RecA amino acid sequence. Gene
  44. Nomenclature for protein modules and their cognate motifs. I n Modular Protein Domains Edited by: Cesareni
  45. (1998). novel colour INteractive editor for multiple alignments. Gene
  46. (2004). Ochman H: Identification and phylogenetic sorting of bacterial lineages with universally conserved genes and proteins. Environ Microbiol
  47. (1980). Organization of the recA gene of Escherichia coli.
  48. (2008). Pavletich NP: Mechanism of homologous recombination from the RecA-ssDNA/dsDNA structures. Nature
  49. (2001). PE: Conserved key amino acid positions (CKAAPs) derived from the analysis of common substructures in proteins. Proteins
  50. (1987). Profile analysis: detection of distantly related proteins.
  51. (1999). Recombinational DNA repair in bacteria and the RecA protein. Prog Nucleic Acid Res Mol Biol
  52. (1982). RF: A simple method for displaying the hydropathic character of a protein.
  53. (1996). RL: Helix propagation and Ncap propensities of the amino acids measured in alaninebased peptides in 40 volume percent trifluoroethanol. Protein Sci
  54. (1994). RL: Helix propensities of the amino acids measured in alanine-based peptides without helix-stabilizing side-chain interactions. Protein Sci
  55. (1985). Roberts JW: Purification of a RecA protein analogue from Bacillus subtilis.
  56. (1997). S: Evolutionary comparisons of RecA-like proteins across all major kingdoms of living organisms.
  57. (1999). Shakhnovich EI: Universally conserved positions in protein folds: reading evolutionary signals about stability, folding kinetics and function.
  58. (1993). Sharp PM: Evolution of the recA gene and the molecular phylogeny of bacteria.
  59. (1995). Siede W: SOS responses and DNA damage tolerance in prokaryotes.
  60. (1991). Site-directed mutagenesis in the Escherichia coli recA gene. Biochimie
  61. (1984). Smithies OS: A comprehensive set of sequence analysis programs for the VAX. Nucleic Acids Res
  62. (1990). Stephens RM: Sequence logos: a new way to display consensus sequences. Nucleic Acids Res
  63. (1993). TA: Structural relationship of bacterial RecA proteins to recombination proteins from bacteriophage T4 and yeast. Science
  64. (1992). TA: The structure of the E. coli RecA protein monomer and polymer. Nature
  65. (2000). The bacterial replicative heliase DnaB evolved from a RecA duplication. Genome Res
  66. (1974). The interpretation of protein structures: total volume, group volume distributions and packing density.
  67. (1976). The nature of the accessible and buried surfaces in proteins.
  68. The PyMOL Molecular Graphics System [http://pymol.source forge.net]
  69. (1995). The RecA protein as a model molecule for molecular systematic studies of bacteria: comparison of trees of RecAs and 16S rRNAs from the same species.
  70. (2004). The triplet code from first principles.
  71. (1966). Theriot L: Mutants of Escherichia coli K-12 defective in DNA repair and in genetic recombination. Genetics
  72. (1994). TJ: CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res
  73. (2008). TJ: Understanding eukaryotic linear motifs and their role in cell signaling and regulation. Front Biosci
  74. (2002). Venkitaraman AR: Insights into DNA recombination from the structure of a RAD51-BRCA2 complex. Nature
  75. (1980). WD: Sequences of the recA gene and protein.
  76. (2001). White O: The Comprehensive Microbial Resource. Nucleic Acids Res
  77. (1992). Whittam TS: Sequencing errors and molecular evolutionary analysis. Mol Biol Evol
  78. (1998). Xue H: A major component approach to presenting consensus sequences. Bioinformatics
  79. (2005). Yaschenko E: Database resources of the National Center for Biotechnology Information. Nucleic Acids Res

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