• RAxML

  • Referenced in 44 articles [sw07716]
  • representative organisms from the three domains: Eukarya, Bacteria and Archaea. Finally, we compare the sequential...
  • BacSim

  • Referenced in 22 articles [sw17261]
  • developed to simulate growth and behaviour of bacteria. The potential of this approach ... making the model easily applicable to various bacteria under different conditions, the model uses...
  • Psortb

  • Referenced in 18 articles [sw11344]
  • method is only applicable to Gram-negative bacteria. The goals of the present work ... level, expand it to include Gram-positive bacteria and then carry out a comparative analysis ... Gram-positive and Gram-negative bacteria and predictive coverage comparable to other tools for whole...
  • SecretP

  • Referenced in 14 articles [sw22470]
  • crucial for bacterial pathogenesis by making bacteria interact with their environments, particularly delivering pathogenic ... symbiotic bacteria into their eukaryotic hosts. Therefore, identification of bacterial secreted proteins becomes an important ... proteins of Gram-negative and Gram-positive bacteria. For the two types of bacteria ... sets of Gram-negative and Gram-positive bacteria, and the prediction results of our method...
  • AFP-Pred

  • Referenced in 24 articles [sw22441]
  • AFPs are present in vertebrates, invertebrates, plants, bacteria, fungi, etc. Although AFPs have a common...
  • SPAdes

  • Referenced in 14 articles [sw17004]
  • Cell Sequencing. The lion’s share of bacteria in various environments cannot be cloned ... assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained...
  • PredLactamase

  • Referenced in 12 articles [sw16470]
  • Lactamases are endogenously produced enzyme that makes bacteria resistant against β-lactam antibiotics by cleaving...
  • GRAPPA

  • Referenced in 12 articles [sw17255]
  • chromosomes of size comparable to those of bacteria, as well as to datasets with complex...
  • BiofilmSim

  • Referenced in 7 articles [sw18050]
  • moving locations (i. e., the bacteria locations). In particular, we incorporate spatially continuous variable viscosity ... order to initialize the positions of bacteria in the biofilm, experimentally obtained three dimensional coordinate ... that treating the spring-like connections between bacteria as Maxwell or Zener elements provides good...
  • RIATA-HGT

  • Referenced in 7 articles [sw17371]
  • rampant among various groups of genes in bacteria. Further, HGT is a major confounding factor...
  • BioOptimizer

  • Referenced in 6 articles [sw17421]
  • sets of co-regulated genes in bacteria. In addition, this scoring function formulation enables...
  • BOMP

  • Referenced in 4 articles [sw11337]
  • proteins encoded within genomes of Gram-negative bacteria. This work describes the development ... barrels per predicted proteome of 10 different bacteria to range from 1.8 to 3%. BOMP...
  • PRED-TMBB

  • Referenced in 5 articles [sw11338]
  • transmembrane beta-strands of the gram-negative bacteria outer membrane proteins, and of discriminating such...
  • TMBpro

  • Referenced in 5 articles [sw11341]
  • outer membranes of mitochondria, Gram-negative bacteria and chloroplasts. These proteins perform critical functions, including...
  • Artemis

  • Referenced in 5 articles [sw17342]
  • useful in analysing the compact genomes of bacteria, archaea and lower eukaryotes, and will cope...
  • OrthoDB

  • Referenced in 5 articles [sw22979]
  • arthropods, 61 vertebrates, 227 fungi and 2627 bacteria (sampling the most complete and representative genomes...
  • PROFtmb

  • Referenced in 4 articles [sw11343]
  • beta-barrel (TMB) proteins in Gram-negative bacteria. For each query protein, PROFtmb provides both...
  • RNAplex

  • Referenced in 4 articles [sw17143]
  • this mechanism. Additionally ncRNA regulation in bacteria is mainly based upon RNA duplex formation. Finding...
  • GNBSL

  • Referenced in 2 articles [sw26874]
  • predict the subcellular location for Gram-negative bacteria proteins. This paper proposes a new integrative ... system (GNBSL--Gram-negative bacteria subcellular localization) for subcellular localization specifized on the Gram-negative ... bacteria proteins. First, the system generates a position-specific frequency matrix (PSFM) and a position...
  • iPHLoc-ES

  • Referenced in 2 articles [sw25871]
  • significantly impact on the functioning of bacteria and can be used in phage based therapy ... functioning of Bacteriophage in the host bacteria depends on its location in those host cells...