• SLAM

  • Referenced in 5 articles [sw17327]
  • SLAM: cross-species gene finding and alignment with a generalized pair hidden Markov model. Comparative ... used to simultaneously find both the gene structure and alignment of two syntenic genomic regions ... which have been used previously for gene finding, and (2) pair hidden Markov models, which ... sequence alignment. We have built a gene finding and alignment program called SLAM, which aligns...
  • GOstat

  • Referenced in 18 articles [sw10975]
  • GOstat: find statistically overrepresented Gene Ontologies within a group of genes. Summary: Modern experimental techniques...
  • EasyGene

  • Referenced in 7 articles [sw17322]
  • paper, we present a new automated gene-finding method, EasyGene, which estimates the statistical significance...
  • GeneMarkS

  • Referenced in 6 articles [sw23024]
  • prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions ... uses an improved version of the gene finding program GeneMark.hmm, heuristic Markov models of coding ... translation starts of GenBank annotated Bacillus subtilis genes and 94.4% of translation starts...
  • FatiGO

  • Referenced in 18 articles [sw12318]
  • FatiGO: a web tool for finding significant associations of Gene ontology terms with groups...
  • Rnamotif

  • Referenced in 10 articles [sw04638]
  • example of applying the code to finding tRNA genes is given...
  • ExonHunter

  • Referenced in 4 articles [sw23816]
  • ExonHunter: A comprehensive approach to gene finding. MOTIVATION: We present ExonHunter, a new and comprehensive ... gene finding system that outperforms existing systems and features several new ideas and approaches ... protein databases of related species) into a gene finder based on a hidden Markov model...
  • Prodigal

  • Referenced in 4 articles [sw16997]
  • algorithm called Prodigal (PROkaryotic DYnamic programming Gene-finding ALgorithm). With Prodigal, we focused specifically ... results of Prodigal to existing gene-finding methods to demonstrate that it met each ... built a fast, lightweight, open source gene prediction program called Prodigal http://compbio.ornl.gov/prodigal/. Prodigal...
  • REPuter

  • Referenced in 16 articles [sw29724]
  • searching for low copy repeats, finding unique sequences, comparing gene structures and mapping of cDNA/EST...
  • mGene

  • Referenced in 4 articles [sw23030]
  • mGene: accurate SVM-based gene finding with an application to nematode genomes. We present ... merely 8%. These findings suggest that even the gene catalog of a well-studied organism ... gene inventions. In a quality assessment of several available annotations for these genomes, we find...
  • GeneRank

  • Referenced in 16 articles [sw27064]
  • data we find that the algorithm offers an improved ranking of genes compared to pure...
  • GOLEM

  • Referenced in 4 articles [sw20340]
  • analysis of an input list of genes to find enriched gene ontology terms. The GOLEM...
  • CoXpress

  • Referenced in 3 articles [sw17858]
  • include a statistical test to find differentially expressed genes, or use of a clustering algorithm ... find groups of genes that behave similarly across a dataset. However, these methods may miss ... coXpress can be used to find groups of genes that display differential co-expression patterns...
  • colcor

  • Referenced in 5 articles [sw12289]
  • discovery rate (FDR) controlling methods to find interesting genes. For example, Z could measure...
  • Digit

  • Referenced in 2 articles [sw01307]
  • Digit: a novel gene finding program by combining gene-finders. We have developed a general ... purpose algorithm which finds genes by combining plural existing gene-finders. The algorithm has been...
  • GeneMark

  • Referenced in 3 articles [sw17182]
  • GeneMark: web software for gene finding in prokaryotes, eukaryotes and viruses. The task of gene...
  • Signal-3L

  • Referenced in 16 articles [sw26857]
  • crucial tool in finding new drugs or reprogramming cells for gene therapy. To effectively...
  • YACOP

  • Referenced in 2 articles [sw17190]
  • starts. Performance of YACOP and the gene-finding programs was tested by comparing their output ... found that the problem of identifying genes in prokaryotic genomes by means of computational analysis...
  • POIMs

  • Referenced in 2 articles [sw35360]
  • many important bioinformatics problems, such as gene finding and function prediction, is the classification...
  • REGANOR

  • Referenced in 1 article [sw23031]
  • implements our previously described, accurate gene finding method REGANOR. We also provide novel gene predictions ... sets are available online. AVAILABILITY: The gene finding server is accessible via https://www.cebitec.uni-bielefeld.de/groups/brf/software/reganor/cgi-bin/reganor_upload.cgi....