• 2L-piRNA

  • Referenced in 25 articles [sw27667]
  • piwi-interacting RNAs, are of small non-coding RNA with around ... length. Given a small non-coding RNA molecule, can we predict whether...
  • Rfam

  • Referenced in 33 articles [sw04637]
  • Rfam database is a collection of RNA families, each represented by multiple sequence alignments, consensus ... down into three broad functional classes: non-coding RNA genes, structured cis-regulatory elements...
  • iMiRNA-PseDPC

  • Referenced in 10 articles [sw22425]
  • microRNA (miRNA) is a small non-coding RNA molecule, functioning in transcriptional and post-transcriptional...
  • PSoL

  • Referenced in 5 articles [sw30044]
  • sample only learning algorithm for finding non-coding RNA genes. Motivation: Small non-coding...
  • mirTools

  • Referenced in 2 articles [sw29588]
  • high-throughput sequencing. miRNAs are small, non-coding RNA that negatively regulate gene expression ... have been applied to investigate various small RNA transcriptomes, their computational methods are far away ... allow researchers to comprehensively characterize small RNA transcriptome. With the aid of mirTools, users ... known categories, such as known miRNAs, non-coding RNA, genomic repeats and coding sequences...
  • STRAL

  • Referenced in 3 articles [sw35516]
  • STRAL: progressive alignment of non-coding RNA using base pairing probability vectors in quadratic time...
  • R-Coffee

  • Referenced in 2 articles [sw17130]
  • method for multiple alignment of non-coding RNA. R-Coffee is a multiple RNA alignment...
  • Cofolga

  • Referenced in 2 articles [sw12674]
  • RNAs. In order to predict non-coding RNA genes and functions on the basis...
  • PETfold

  • Referenced in 1 article [sw17126]
  • multiple RNA sequences. The function of non-coding RNA genes largely depends on their secondary...
  • CMfinder

  • Referenced in 6 articles [sw17265]
  • numbers of non-coding RNAs and computational advances in genome-scale RNA search create...
  • LncmiRSRN

  • Referenced in 1 article [sw34139]
  • LncmiRSRN: identification and analysis of long non-coding RNA related miRNA sponge regulatory network...
  • starBase

  • Referenced in 10 articles [sw23121]
  • RNA interaction networks from large-scale CLIP-Seq data. Although microRNAs (miRNAs), other non-coding ... v2.0 (http://starbase.sysu.edu.cn/) to systematically identify the RNA-RNA and protein-RNA interaction networks from...
  • LncFinder

  • Referenced in 0 articles [sw18819]
  • package LncFinder. LncFinder: Long Non-Coding RNA Identification Based on Features of Sequence, EIIP ... predicting sequences are mRNAs or long non-coding RNAs. Default models are trained on human...
  • PETcofold

  • Referenced in 3 articles [sw17127]
  • RNA interactions is essential for determining the function of putative non-coding RNAs. Existing methods ... comparative methods have already been useful in RNA structure determination, we assume that conserved...
  • LncPath

  • Referenced in 0 articles [sw15466]
  • regulated by the interested lncRNA(long non-coding RNA) sets based on a lncRNA-mRNA...
  • RILogo

  • Referenced in 1 article [sw17139]
  • amount of newly discovered non-coding RNAs, the interactions between RNA molecules become an increasingly...
  • IntaRNA

  • Referenced in 2 articles [sw29324]
  • RNA molecules. It has been designed to predict mRNA target sites for given non-coding ... used to predict other types of RNA-RNA interactions. Precomputed results for Enterobacteria: ChiX, CyaR...
  • CentroidAlign

  • Referenced in 2 articles [sw17119]
  • RNA sequences has increased due to recent findings about functional non-coding RNAs. Recent studies ... accuracy (MEA) estimator for pairwise alignment of RNA sequences. This maximizes the expected...
  • psRNATarget

  • Referenced in 1 article [sw34140]
  • plant small RNA target analysis server. Plant endogenous non-coding short small RNAs ... present psRNATarget, a plant small RNA target analysis server, which features two important analysis functions...
  • RactIP

  • Referenced in 2 articles [sw17120]
  • RNA interaction since it is a key to identifying possible targets of non-coding small ... fast and accurate prediction method for RNARNA interaction of general type using integer programming...