• GOASVM

  • Referenced in 6 articles [sw22445]
  • selected GO terms in the Gene Ontology annotation (GOA) database as a means to construct...
  • ASTALAVISTA

  • Referenced in 3 articles [sw17177]
  • custom gene datasets. In the process of establishing more and more complete annotations of eukaryotic ... extracts AS events dynamically from custom gene annotations, classifies them into groups of common types ... data from reference annotations (GENCODE, REFSEQ, ENSEMBL) as well as for genes selected...
  • Cytoscape

  • Referenced in 82 articles [sw09080]
  • link the network to databases of functional annotations. The Core is extensible through a straightforward ... interaction pathways correlating with changes in gene expression, a study of protein complexes involved...
  • OrthoDB

  • Referenced in 5 articles [sw22979]
  • become instrumental for generating hypotheses about gene functions crucial to many studies. This update ... most extensive integration of functional annotations from UniProt, InterPro, GO, OMIM, model organism phenotypes ... annotations including rates of ortholog sequence divergence, copy-number profiles, sibling groups and gene architectures ... genes, proteins, domains, ontologies or annotation keywords and phrases. Gene copy-number profiles can also...
  • miRBase

  • Referenced in 23 articles [sw14367]
  • annotation data are also available for download. The miRBase Registry provides miRNA gene hunters with...
  • lumi

  • Referenced in 3 articles [sw08431]
  • quality control, variance stabilization, normalization and gene annotation portions. In specific, the lumi package includes...
  • GeneCards

  • Referenced in 8 articles [sw30714]
  • GeneCards®: The Human Gene Database. GeneCards is a searchable, integrative database that provides comprehensive ... user-friendly information on all annotated and predicted human genes. It automatically integrates gene-centric...
  • biomaRt

  • Referenced in 3 articles [sw17280]
  • range of powerful online queries from gene annotation to database mining...
  • GOLEM

  • Referenced in 4 articles [sw20340]
  • interactively expandable graph-based view of the gene ontology hierarchy. Furthermore, most existing tools ... Internet connection, will not load local annotations files, and provide either analysis or visualization functionality ... user either to utilize local gene ontology and annotations files in the absence ... most recent ontology and annotation information from the gene ontology webpage. GOLEM supports global...
  • ANNOVAR

  • Referenced in 4 articles [sw17295]
  • annotate single nucleotide variants (SNVs) and insertions/deletions, such as examining their functional consequence on genes ... Genomes Project and dbSNP. ANNOVAR can utilize annotation databases from the UCSC Genome Browser ... annotation data set conforming to Generic Feature Format version 3 (GFF3). We also illustrate ... ANNOVAR requires ∼4 min to perform gene-based annotation and ∼15 min to perform variants...
  • ARFA

  • Referenced in 2 articles [sw35517]
  • ARFA: a program for annotating bacterial release factor genes, including ... prediction of programmed ribosomal frameshifting . Correct annotation of genes encoding release factors in bacterial genomes ... program identifies and automatically annotates +1 frameshifting in RF2 encoding genes. Comparison of ARFA performance ... genes utilizing ribosomal frameshifting during their expression are annotated correctly...
  • GeneMarkS

  • Referenced in 6 articles [sw23024]
  • implementation uses an improved version of the gene finding program GeneMark.hmm, heuristic Markov models ... translation starts of GenBank annotated Bacillus subtilis genes and 94.4% of translation starts...
  • Exogean

  • Referenced in 2 articles [sw17149]
  • Exogean: a framework for annotating protein-coding genes in eukaryotic genomic DNA. Background: Accurate ... automatic gene identification in eukaryotic genomic DNA is more than ever of crucial importance ... illustrated in the EGASP project, where reference annotations against which all automatic methods are measured ... method that best reproduces protein coding gene annotations from human experts, in terms of identifying...
  • GENECODIS

  • Referenced in 3 articles [sw13895]
  • based tool for finding significant concurrent annotations in gene lists. We present GENECODIS ... search for annotations that frequently co-occur in a set of genes and rank them ... statistical significance. The analysis of concurrent annotations provides significant information for the biologic interpretation ... standard methods for the functional analysis of gene lists. GENECODIS is publicly available...
  • GFINDer

  • Referenced in 3 articles [sw13898]
  • through dynamic annotation, statistical analysis, and mining. Statistical and clustering analyses of gene expression results ... tools have been developed for annotating lists of genes, most of them do not give ... annotations provided, or for estimating the functional bias introduced by the gene ... characterizing the different gene classes in the list. GFINDer automatically retrieves annotations of several functional...
  • AceView

  • Referenced in 3 articles [sw23000]
  • Gene names when available, else by AceView gene names, stable from release to release. Alternative ... potential, including motifs, domains, and homologies are annotated in depth; tissues where expression has been ... PubMed, GAD and Entrez Gene, and also by performing manual annotation, especially in the worm ... supported human, mouse and nematode genes are thoroughly annotated. Our goals are to offer...
  • Virus-ploc

  • Referenced in 14 articles [sw22421]
  • annotated for their subcellular locations in this regard. As for the gene ontology database ... development of high throughput tools for timely annotating the localization of viral proteins within host...
  • Transcriptator

  • Referenced in 2 articles [sw22343]
  • TRANSCRIPTATOR is a computational pipeline to functionally annotate differentially expressed transcripts and carry ... statistical analysis of functional and gene ontology annotation enrichment; identification of enriched biological themes, particularly ... annotation; tabular report for functional and gene ontology annotation for each and every transcripts submitted...
  • GOSim

  • Referenced in 5 articles [sw08204]
  • need to further explore the similarity of genes not only with respect to their expression ... respect to their functional annotation which can be obtained from Gene Ontology (GO). GOSim Package ... given grouping of genes with respect to their GO annotation. GOSim hence provides the researcher...
  • I-TASSER

  • Referenced in 18 articles [sw17207]
  • functional annotations on ligand-binding sites, Enzyme Commission numbers and Gene Ontology terms. An estimate...