• Rfam

  • Referenced in 32 articles [sw04637]
  • Rfam database is a collection of RNA families, each represented by multiple sequence alignments, consensus ... covariance models (CMs). The families in Rfam break down into three broad functional classes ... structure in an elegant and accurate fashion. Rfam families are frequently built from external sources ... your work that you cite both Rfam and the primary source of our data...
  • MODENA

  • Referenced in 5 articles [sw23804]
  • with 29 target structures taken from the Rfam database, and we found that MODENA...
  • MARNA

  • Referenced in 5 articles [sw35539]
  • MARNA on several datasets taken from the Rfam database. Availability: MARNA can be used online...
  • RNAspa

  • Referenced in 2 articles [sw17131]
  • include several ncRNA families taken from the Rfam database. These datasets allowed for comparison...
  • PMFastR

  • Referenced in 1 article [sw24608]
  • programs. Furthermore, we regenerate 607 Rfam seed alignments and show that our automated process creates ... similar multiple alignments to the manually-curated Rfam seed alignments...
  • PETfold

  • Referenced in 1 article [sw17126]
  • annotated RNA alignments, such as the Rfam 10.0 database and multiple alignments of 16 vertebrate...
  • RNASTAR

  • Referenced in 1 article [sw17132]
  • improved alignments have been contributed to the Rfam database...
  • NoFold

  • Referenced in 1 article [sw23125]
  • empirically defined structure model (e.g. Rfam family covariance models). NoFold provides scripts for mapping sequences...
  • R

  • Referenced in 8180 articles [sw00771]
  • R is a language and environment for statistical...
  • STAR

  • Referenced in 12 articles [sw02515]
  • STAR: ultrafast universal RNA-seq aligner. Motivation: Accurate...
  • Bioconductor

  • Referenced in 291 articles [sw04205]
  • Bioconductor provides tools for the analysis and comprehension...
  • edgeR

  • Referenced in 46 articles [sw06936]
  • edgeR: a Bioconductor package for differential expression analysis...
  • RNAshapes

  • Referenced in 7 articles [sw07960]
  • RNAshapes: an integrated RNA analysis package based on...
  • onechannelgui

  • Referenced in 3 articles [sw07962]
  • oneChannelGUI: A graphical interface designed to facilitate analysis...
  • BaySeq

  • Referenced in 17 articles [sw10343]
  • baySeq: Empirical Bayesian analysis of patterns of differential...
  • EMBOSS

  • Referenced in 34 articles [sw10917]
  • EMBOSS is ”The European Molecular Biology Open Software...
  • ClustalW

  • Referenced in 133 articles [sw12016]
  • CLUSTAL W: improving the sensitivity of progressive multiple...
  • Mfold

  • Referenced in 41 articles [sw12672]
  • Mfold web server for nucleic acid folding and...
  • KEGG

  • Referenced in 250 articles [sw13866]
  • KEGG: Kyoto Encyclopedia of Genes and Genomes. KEGG...