Gapped BLAST and PSI-BLAST: a new generation of protein database search programs

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Items 801–900 of 1,546

1. Finding the genes in genomic DNA
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3. Dynamin and the Actin Cytoskeleton Cooperatively Regulate Plasma Membrane Invagination by BAR and F-BAR Proteins
   Toshiki Itoh, Kai S. Erdmann, Aurélien Roux, Bianca Hermine Habermann, Hauke B. Werner, Pietro V. De Camilli · 2005 · Developmental Cell
4. The virophage as a unique parasite of the giant mimivirus
   Bernard La Scola, Christelle Desnues, Isabelle Pagnier, Catherine Robert, Lina Barrassi, Ghislain Fournous, Michèle Merchat, Marie Suzan, Patrick Forterre, Eugene V. Koonin et al. · 2008 · Nature
5. Siderophore-mediated signaling regulates virulence factor production in <i>Pseudomonas</i> <i>aeruginosa</i>
   Lamont, Iain L., Beare, Paul A., Ochsner, Urs, Vasil, Adriana I., Vasil, Michael L. · 2002 · Proceedings of the National Academy of Sciences
6. Galectinomics: finding themes in complexity
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7. M ercator: a fast and simple web server for genome scale functional annotation of plant sequence data
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8. PredictProtein—an open resource for online prediction of protein structural and functional features
   Guy Yachdav, Edda Kloppmann, László Kaján, Maximilian Hecht, Tatyana Goldberg, Tobias Hamp, Peter Hönigschmid, Andrea Schafferhans, Manfred Roos, Michael Bernhofer et al. · 2014 · Nucleic Acids Research
9. Isolation and Identification of Actinobacteria from Surface-Sterilized Wheat Roots
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10. Widespread and Persistent Populations of a Major New Marine Actinomycete Taxon in Ocean Sediments
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11. Database resources of the National Center for Biotechnology Information
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12. A genomic timescale of prokaryote evolution: insights into the origin of methanogenesis, phototrophy, and the colonization of land
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13. The Magnaporthe oryzae Effector AvrPiz-t Targets the RING E3 Ubiquitin Ligase APIP6 to Suppress Pathogen-Associated Molecular Pattern–Triggered Immunity in Rice
    Chan Ho Park, Songbiao Chen, Gautam S. Shirsekar, Bo Zhou, Chang Hyun Khang, Pattavipha Songkumarn, Ahmed Jawaad Afzal, Yuese Ning, Ruyi Wang, Maria del Rosario Bellizzi et al. · 2012 · The Plant Cell
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15. Protein interaction mapping: ADrosophilacase study
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16. Charting the Proteomes of Organisms with Unsequenced Genomes by MALDI-Quadrupole Time-of-Flight Mass Spectrometry and BLAST Homology Searching
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17. Biodiversity of Denitrifying and Dinitrogen-Fixing Bacteria in an Acid Forest Soil
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18. Improved reference genome of Aedes aegypti informs arbovirus vector control
    Benjamin John Matthews, Olga Dudchenko, Sarah B. Kingan, Sergey Koren, Igor A. Antoshechkin, Jacob E. Crawford, William J. Glassford, Margaret Herre, Seth N. Redmond, Noah H. Rose et al. · 2018 · Nature
19. Microglia serve as a neuroimmune substrate for stress-induced potentiation of CNS pro-inflammatory cytokine responses
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20. The mouse stargazer gene encodes a neuronal Ca2+-channel γ subunit
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21. Identification, analysis, and prediction of protein ubiquitination sites
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22. Development of microsatellite markers in peach [Prunus persica (L.) Batsch] and their use in genetic diversity analysis in peach and sweet cherry (Prunus avium L.)
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23. Dissecting the bacterial type VI secretion system by a genome wide in silico analysis: what can be learned from available microbial genomic resources?
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24. Distinguishing Enzyme Structures from Non-enzymes Without Alignments
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25. MyTaxa: an advanced taxonomic classifier for genomic and metagenomic sequences
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26. Temporal Patterns of Fruit Fly (Drosophila) Evolution Revealed by Mutation Clocks
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27. Folding non-homologous proteins by coupling deep-learning contact maps with I-TASSER assembly simulations
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28. miREvo: an integrative microRNA evolutionary analysis platform for next-generation sequencing experiments
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29. Predicting protein function from sequence and structure
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30. Validating internal controls for quantitative plant gene expression studies
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31. The t(4;14) Translocation in Myeloma Dysregulates Both FGFR3and a Novel Gene, MMSET, Resulting in IgH/MMSET Hybrid Transcripts
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32. The Arabidopsis thaliana Chloroplast Proteome Reveals Pathway Abundance and Novel Protein Functions
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33. Differences in the composition of vaginal microbial communities found in healthy Caucasian and black women
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34. A Novel Electrochemically Active and Fe(III)-reducing Bacterium Phylogenetically Related to Clostridium butyricum Isolated from a Microbial Fuel Cell
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35. eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges
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36. Metagenomic and Small-Subunit rRNA Analyses Reveal the Genetic Diversity of Bacteria, Archaea, Fungi, and Viruses in Soil
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37. New neuropeptides containing carboxy-terminal RFamide and their receptor in mammals
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38. Genomewide comparative analysis of alternative splicing in plants
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39. Potential for Direct Interspecies Electron Transfer in Methanogenic Wastewater Digester Aggregates
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40. Enhancement of protein modeling by human intervention in applying the automatic programs 3D-JIGSAW and 3D-PSSM
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41. Pyrosequencing of Antibiotic-Contaminated River Sediments Reveals High Levels of Resistance and Gene Transfer Elements
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42. Importance of Lineage-Specific Expansion of Plant Tandem Duplicates in the Adaptive Response to Environmental Stimuli
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43. A ubiquitous family of putative gap junction molecules
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44. Highly evolvable malaria vectors: The genomes of 16 Anopheles mosquitoes
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45. Mismatch string kernels for discriminative protein classification
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46. DeepGO: predicting protein functions from sequence and interactions using a deep ontology-aware classifier
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47. The GAF domain: an evolutionary link between diverse phototransducing proteins
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48. Global dissemination of a multidrug resistant Escherichia coli clone
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49. Competitive and cooperative metabolic interactions in bacterial communities
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50. Common Origin of Four Diverse Families of Large Eukaryotic DNA Viruses
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51. The Rice Resistance Protein Pair RGA4/RGA5 Recognizes the Magnaporthe oryzae Effectors AVR-Pia and AVR1-CO39 by Direct Binding
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52. Protein Secondary Structure Prediction Using Deep Convolutional Neural Fields
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53. Membrane topology and mitochondrial targeting of mitofusins, ubiquitous mammalian homologs of the transmembrane GTPase Fzo
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54. Sequence comparisons using multiple sequences detect three times as many remote homologues as pairwise methods
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55. Muricauda ruestringensis gen. nov., sp. nov., a facultatively anaerobic, appendaged bacterium from German North Sea intertidal sediment.
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56. Development of an epitope conservancy analysis tool to facilitate the design of epitope-based diagnostics and vaccines
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57. PrankWeb: a web server for ligand binding site prediction and visualization
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58. Intergenomic Comparisons Highlight Modularity of the Denitrification Pathway and Underpin the Importance of Community Structure for N2O Emissions
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59. Exploiting heterogeneous sequence properties improves prediction of protein disorder
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60. Protein Structure and Function Prediction Using I‐TASSER
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61. RaptorX-Property: a web server for protein structure property prediction
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62. Mechanosensitive ion channels: molecules of mechanotransduction
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63. GenBank
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64. ConSurf: Using Evolutionary Data to Raise Testable Hypotheses about Protein Function
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65. A structural classification of substrate‐binding proteins
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66. 454 Pyrosequencing and Sanger sequencing of tropical mycorrhizal fungi provide similar results but reveal substantial methodological biases
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67. Multiple evidence strands suggest that there may be as few as 19 000 human protein-coding genes
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68. Calmodulin Target Database
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69. Endophytic and ectophytic potato-associated bacterial communities differ in structure and antagonistic function against plant pathogenic fungi
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70. Size Selective Recognition of siRNA by an RNA Silencing Suppressor
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71. Introducing EzAAI: a pipeline for high throughput calculations of prokaryotic average amino acid identity
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72. Molecular characterization of Ph1 as a major chromosome pairing locus in polyploid wheat
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73. From algae to angiosperms–inferring the phylogeny of green plants (Viridiplantae) from 360 plastid genomes
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74. A Telomeric Avirulence Gene Determines Efficacy for the Rice Blast Resistance Gene Pi-ta
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75. The ring of life provides evidence for a genome fusion origin of eukaryotes
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76. Evolutionary origins of eukaryotic sodium/proton exchangers
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77. Essential Genes Are More Evolutionarily Conserved Than Are Nonessential Genes in Bacteria
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78. Predicting multiple conformations via sequence clustering and AlphaFold2
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79. Changes in coral-associated microbial communities during a bleaching event
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80. The Isolation of Antibiotic-Resistant Salmonella from Retail Ground Meats
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81. Predominant archaea in marine sediments degrade detrital proteins
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85. Alignment-free sequence comparison: benefits, applications, and tools
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86. The Arabidopsis DELAYED DEHISCENCE1 Gene Encodes an Enzyme in the Jasmonic Acid Synthesis Pathway
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87. Rab‐interacting lysosomal protein (RILP): the Rab7 effector required for transport to lysosomes
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88. Comparative genomics of the major parasitic worms
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89. Comparative genomics and evolution of proteins involved in RNA metabolism
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90. The SPOROCYTELESS gene of Arabidopsis is required for initiation of sporogenesis and encodes a novel nuclear protein
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94. Colonization, biofilm formation and biodegradation of polyethylene by a strain of Rhodococcus ruber
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95. Ray: Simultaneous Assembly of Reads from a Mix of High-Throughput Sequencing Technologies
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97. Performance of mutation pathogenicity prediction methods on missense variants
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99. High-throughput prediction of protein antigenicity using protein microarray data
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100. CHAINSAW: a program for mutating pdb files used as templates in molecular replacement
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