• iPro54-PseKNC

  • Referenced in 32 articles [sw22411]
  • promoters are unique in prokaryotic genome and responsible for transcripting carbon and nitrogen-related genes...
  • OrthoMCL

  • Referenced in 15 articles [sw29602]
  • restricted sequences. Methods successfully exploited for prokaryotic genome analysis have proved difficult to apply...
  • GeneMark

  • Referenced in 8 articles [sw17182]
  • GeneMark: web software for gene finding in prokaryotes, eukaryotes and viruses. The task of gene ... tuned for gene prediction in prokaryotic, eukaryotic and viral genomic sequences. Currently, the server allows ... analysis of nearly 200 prokaryotic and >10 eukaryotic genomes using species-specific versions ... models. In addition, genes in prokaryotic sequences from novel genomes can be identified using models...
  • EasyGene

  • Referenced in 7 articles [sw17322]
  • random Open Reading Frames (ORFs) in prokaryotic genomes. Therefore, many genomes have too many short...
  • GeneMarkS

  • Referenced in 6 articles [sw23024]
  • prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions ... remaining open problems in computer prediction of prokaryotic genes. Its difficulty is caused ... used for a newly sequenced prokaryotic genome with no prior knowledge of any protein ... have also observed that GeneMarkS detects prokaryotic genes, in terms of identifying open reading frames...
  • HPAM

  • Referenced in 3 articles [sw10931]
  • hybrid promoter analysis methodology for prokaryotic genomes. One of the big challenges of the post ... genomic era is identifying regulatory systems and integrating them into genetic networks. Gene expression ... predicting the RNA polymerase motif in prokaryotic genomes. This constitutes a special challenge...
  • MetaGeneAnnotator

  • Referenced in 3 articles [sw17338]
  • precise gene prediction in anonymous prokaryotic and phage genomes. Recent advances in DNA sequencers ... especially in microbes, and complete and draft genomes from various species have been sequenced ... kinds of prokaryotic genes from a single or a set of anonymous genomic sequences having ... transferred and prophage genes in a prokaryotic genome. In this paper, we also propose...
  • PILER

  • Referenced in 3 articles [sw35547]
  • program executes rapidly, completing a 5 Mb genome in around 5 seconds on a current ... comprehensive analysis of 346 prokaryotic genomes. Conclusion: PILER-CR is a useful tool for rapid...
  • TICO

  • Referenced in 3 articles [sw23022]
  • results of conventional gene finders for prokaryotic genomes with regard to exact localization...
  • CVTree3

  • Referenced in 6 articles [sw22015]
  • Server for Whole-genome-based and Alignment-free Prokaryotic Phylogeny and Taxonomy. A faithful phylogeny ... taxonomy for prokaryotes should agree with each other and ultimately follow the genome data. With ... alignment-free and whole-genome-based web server CVTree3. The server resides in a cluster ... classification of prokaryotes and determination of taxonomic placement of some newly-sequenced genomes...
  • REGANOR

  • Referenced in 1 article [sw23031]
  • REGANOR: a gene prediction server for prokaryotic genomes and a database of high quality gene ... predictions for prokaryotes. With >1,000 prokaryotic genome sequencing projects ongoing or already finished, comprehensive ... resource for gene identification in prokaryote genome sequences. It implements our previously described, accurate gene ... complete, or almost complete, prokaryotic genomes. We demonstrate how this resource can easily be utilised...
  • YACOP

  • Referenced in 2 articles [sw17190]
  • problem of identifying genes in prokaryotic genomes by means of computational analysis was solved satisfactorily...
  • CAR

  • Referenced in 1 article [sw34564]
  • contig assembly of prokaryotic draft genomes using rearrangements. Background: Next generation sequencing technology has allowed ... orient the contigs of a prokaryotic draft genome based on a reference genome ... real dataset composed of several prokaryotic genomes and also compared its performance with several other ... orient the contigs of a prokaryotic draft genome based on a reference genome...
  • Prokka

  • Referenced in 2 articles [sw16996]
  • Prokka: rapid prokaryotic genome annotation. Summary: The multiplex capability and high yield of current...
  • Prophinder

  • Referenced in 2 articles [sw35322]
  • computational tool for prophage prediction in prokaryotic genomes. Summary: Prophinder is a prophage prediction tool...
  • BRIG

  • Referenced in 1 article [sw22991]
  • BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons. Conclusions: There is a clear need ... comparisons for a large number of prokaryote genomes with an emphasis on rapidly utilising unfinished...
  • BioProspector

  • Referenced in 29 articles [sw09375]
  • sequences or pre-computed from the whole genome sequences. A new motif scoring function ... patterns, which are prevalent motif patterns in prokaryotes. All these modifications greatly improve the performance ... find s54 motif from M. xanthus genome, many B. subtilis motifs from DBTBS collection...
  • ODoSE

  • Referenced in 1 article [sw16945]
  • Webserver for Genome-Wide Calculation of Adaptive Divergence in Prokaryotes. Quantifying patterns of adaptive divergence ... comparative and evolutionary study of prokaryote genomes. When applied appropriately, the McDonald-Kreitman (MK) test ... evolutionary forces shaping core genome divergence in prokaryotes. ODoSE is hosted in a Galaxy environment...
  • PRAP

  • Referenced in 1 article [sw23830]
  • Package for Automated Genome Wide Analysis of DNA Repeats for Prokaryotes. PRAP (Prokaryotic Repeats Annotation ... repeats in both finished and drafted genomes. It aimed ... identifying full spectrum repeats at the prokaryote genome scale. The final output is parsed into ... other genome data. It is currently the most complete repeat finder for prokaryote...
  • PGAT

  • Referenced in 1 article [sw08338]
  • PGAT: Prokaryotic Genome Analysis Tool. PGAT is designed to facilitate comparative analysis of closely related...