• Infernal

  • Referenced in 11 articles [sw17000]
  • family called covariance models (CMs) from structurally annotated multiple sequence alignments given as input. Infernal ... filter pipeline for RNA homology search based on accelerated profile hidden Markov model (HMM) methods...
  • LocARNAscan

  • Referenced in 2 articles [sw23118]
  • structure-based RNA homology search. BACKGROUND: The search for distant homologs has become an import ... issue in genome annotation. A particular difficulty is posed by divergent homologs that have lost ... common descent. Current homology search tools for structured RNAs are either based entirely on sequence ... demonstrate that a purely structure-based homology search is feasible in principle, it is unlikely...
  • HAMAP

  • Referenced in 1 article [sw22977]
  • allows for precise annotation of individual functional variants within large homologous protein families. We also ... describe improvements to our web-based tool HAMAP-Scan which simplify the classification and annotation...
  • Hum-PLoc

  • Referenced in 19 articles [sw26863]
  • amphiphilic pseudo amino acid composition (PseAA). Based on such a representation frame, a novel ensemble ... membrane. To get rid of redundancy and homology bias, none of the proteins investigated here ... trivial utilization of the GO annotations. This is because, for those proteins with ”subcellular location...
  • Euk-PLoc

  • Referenced in 21 articles [sw22420]
  • database and amphiphilic pseudo amino acid composition. Based on such a representation, a novel ensemble ... body, and (18) vacuole. To avoid the homology bias, none of the proteins included ... database that do not have subcellular location annotations or are annotated as being uncertain...
  • GeneReporter

  • Referenced in 2 articles [sw24071]
  • GeneReporter - sequence-based document retrieval and annotation. GeneReporter is a web tool that reports functional ... purpose is to support both manual genome annotation and document retrieval. PubMed references corresponding ... query words from UniProt entries of homologous sequences. Data on protein families, domains, potential cofactors ... integrates databases and analysis tools as SOAP-based web services from the EBI (European Bioinformatics...
  • GOASVM

  • Referenced in 6 articles [sw22445]
  • methods based on other features. Existing GO-based methods, however, do not fully ... from the GO term frequencies and distant homologs to represent a protein in the general ... protein or the ACs of its homologs to find the number of occurrences ... selected GO terms in the Gene Ontology annotation (GOA) database as a means to construct...
  • piRNAQuest

  • Referenced in 1 article [sw23007]
  • comprehensive and unified database provides annotation of piRNAs based on their genomic location in Gene ... cluster. Several analysis tools like Homology search within annotated piRNAs, Dynamic piRNA Clusters, Pattern Search...
  • FragGeneScan

  • Referenced in 4 articles [sw17159]
  • become an important yet challenging problem in annotating metagenomes, since the assembly of metagenomes ... bases with 1% sequencing errors, and ∼18% for short reads of 100 bases that ... predicted (>90% of the genes identified by homology search), and many novel genes with...
  • RILogo

  • Referenced in 1 article [sw17139]
  • homologous sequences. Here, we present RILogo, a program to visualize inter- and intramolecular base pairing ... RILogo is a pair of structure-annotated sequences or alignments. In the latter case, RILogo...
  • MemLoci

  • Referenced in 2 articles [sw24068]
  • localization is inferred on the basis of annotation transfer upon sequence similarity search. However, predictive ... tools are necessary when the localization of homologs is not known. This is so particularly ... develop MemLoci, a new support vector machine-based tool that discriminates three membrane protein localizations...
  • LEON

  • Referenced in 2 articles [sw24616]
  • novel method, LEON, to predict homology between proteins based on a multiple alignment of complete ... useful for automatic high-throughput genome annotations, 2D/3D structure predictions, protein–protein interaction predictions...
  • Conrad

  • Referenced in 1 article [sw23028]
  • best standalone gene predictors, which are based on generalized hidden Markov models (GHMMs) and trained ... trained to maximize annotation accuracy. In addition, unlike the best annotation pipelines, which rely ... additional information such as ESTs and protein homology, Conrad encodes all sources of information...
  • PIRSF

  • Referenced in 1 article [sw22978]
  • homeomorphic family, whose members are both homologous (evolved from a common ancestor) and homeomorphic (sharing ... domain architecture). PIRSF families are curated systematically based on literature review and integrative sequence ... pattern. The results of classification and expert annotation are summarized in PIRSF family reports with...
  • PSLDoc

  • Referenced in 1 article [sw24765]
  • annotation, protein function prediction, and drug discovery. Many computational approaches for PSL prediction based ... negative bacteria. We present PSLDoc, a method based on gapped-dipeptides and probabilistic latent semantic ... there is a strong correlation between sequence homology and subcellular localization (Nair and Rost, Protein...
  • Coq

  • Referenced in 1751 articles [sw00161]
  • Coq is a formal proof management system. It...
  • R

  • Referenced in 7624 articles [sw00771]
  • R is a language and environment for statistical...
  • MIRA

  • Referenced in 1 article [sw02392]
  • MIRA is a multi-pass DNA sequence data...
  • STAR

  • Referenced in 11 articles [sw02515]
  • STAR: ultrafast universal RNA-seq aligner. Motivation: Accurate...