• OrthoMCL

  • Referenced in 15 articles [sw29602]
  • orthologous groups is useful for genome annotation, studies on gene/protein evolution, comparative genomics ... INPARANOID algorithm when applied to two genomes, but can be extended to cluster orthologs from ... reliability, implying utility for automated eukaryotic genome annotation. OrthoMCL has been applied to the proteome ... incompletely annotated in first-pass annotation of the parasite genome...
  • iDNA-Prot

  • Referenced in 16 articles [sw22410]
  • major challenges in the field of genome annotation. Although many efforts have been made...
  • BEDTools

  • Referenced in 11 articles [sw17302]
  • genomic features is a fundamental task in genomics research. However, searching for overlaps between features ... suite for the comparison, manipulation and annotation of genomic features in Browser Extensible Data ... data) with both public and custom genome annotation tracks. BEDTools can be combined with ... with standard UNIX commands, thus facilitating routine genomics tasks as well as pipelines that...
  • ESLpred

  • Referenced in 20 articles [sw22403]
  • important step in the functional annotation of genomes. The existing subcellular localization prediction methods ... sequence against the dataset of proteins (experimentally annotated proteins) to predict its subcellular location...
  • Galaxy

  • Referenced in 12 articles [sw16927]
  • that combines the power of existing genome annotation databases with a simple Web portal...
  • starBase

  • Referenced in 10 articles [sw23121]
  • target sites. By combining 13 functional genomic annotations, we developed miRFunction and ceRNAFunction web servers...
  • UniProt

  • Referenced in 131 articles [sw21320]
  • important collection of protein sequences and their annotations, which has doubled in size ... with the majority of sequences coming from genome sequencing projects. We have created ... experience design process. We have introduced an annotation score for all entries in UniProt...
  • Segmentor3IsBack

  • Referenced in 7 articles [sw21077]
  • exact segmentation of Seq-data. Genome annotation is an important issue in biology which ... coding or non-coding regions of the genome, using an oracle penalty. We illustrate...
  • STAR

  • Referenced in 9 articles [sw35644]
  • they are not systematically detected nor annotated in genome projects. Partially because of this lack...
  • PLINK

  • Referenced in 64 articles [sw04581]
  • PLINK is a free, open-source whole genome association analysis toolset, designed to perform ... some support for the subsequent visualization, annotation and storage of results...
  • GOtcha

  • Referenced in 4 articles [sw17189]
  • protein function assessed by the annotation of seven genomes. Background: The function of a novel ... annotation. Results: The GOtcha method was applied to the recently sequenced genome for Plasmodium falciparum ... method is a useful tool for genome annotators. It has identified both errors and omissions ... original Plasmodium falciparum annotation and is being adopted by many other genome sequencing projects...
  • ProSOM

  • Referenced in 3 articles [sw13019]
  • physical profiles. Motivation: More and more genomes are being sequenced, and to keep up with ... most challenging problems in genome annotation is the identification of the core promoter. Because ... integrate transcription start site prediction in genome annotation projects. Nevertheless, better core promoter prediction ... improve genome annotation and can be used to guide experimental work. Results: Comparing the average...
  • REDfly

  • Referenced in 5 articles [sw29315]
  • species. Drosophila melanogaster, with its well-annotated genome, exceptional resources for comparative genomics and long ... into a single integrated database containing extensive annotation of empirically validated cis-regulatory modules...
  • mGene

  • Referenced in 4 articles [sw23030]
  • were not contained in the current genome annotation. Testing a subset of 57 of these ... quality assessment of several available annotations for these genomes, we find that mGene’s predictions...
  • MAVG

  • Referenced in 9 articles [sw10918]
  • islands in a genomic sequence, and annotating multiple sequence alignments. Availability: http://iubio.bio.indiana.edu/soft/molbio/pattern/cpg_islands/...
  • ChromHMM

  • Referenced in 4 articles [sw29058]
  • then be used to systematically annotate a genome in one or more cell types ... state enrichments for large-scale functional and annotation datasets ChromHMM facilitates the biological characterization ... also produces files with genome-wide maps of chromatin state annotations that can be directly...
  • Apollo

  • Referenced in 2 articles [sw17335]
  • inaccuracy of purely computational methods for annotating genome sequences necessitates an interactive tool to allow ... this need, enabling curators to inspect genome annotations closely and edit them. FlyBase biologists successfully ... used Apollo to annotate the Drosophila melanogaster genome and it is increasingly being used ... development of customized annotation editing tools for other genome projects...
  • SUPERFAMILY

  • Referenced in 5 articles [sw16889]
  • annotation for all proteins and genomes. The SUPERFAMILY annotation is based on a collection ... annotation is produced by scanning protein sequences from over 2,478 completely sequenced genomes against...
  • FlyBase

  • Referenced in 2 articles [sw23002]
  • assembly and large-scale migration of genome annotations. Release 6, the latest reference genome assembly ... information now attached to the D. melanogaster genome in public repositories and individual laboratories ... major event requiring careful migration of annotations and genome-anchored data to the new, improved ... genome assembly, the migration of FlyBase genome annotations to this new assembly, how genome features...
  • MAKER

  • Referenced in 2 articles [sw17331]
  • easy-to-use annotation pipeline designed for emerging model organism genomes. We have ... developed a portable and easily configurable genome annotation pipeline called MAKER. Its purpose ... allow investigators to independently annotate eukaryotic genomes and create genome databases. MAKER identifies repeats, aligns ... principle, we have used MAKER to annotate the genome of the planarian Schmidtea mediterranea...