• Pse-in-One

  • Referenced in 41 articles [sw22407]
  • various modes of pseudo components of DNA, RNA, and protein sequences. With the avalanche ... biological sample (such as DNA, RNA or protein) with a discrete model or a vector ... possible feature vectors for DNA, RNA and protein sequences. Particularly, it can also generate those...
  • Rfam

  • Referenced in 33 articles [sw04637]
  • Rfam database is a collection of RNA families, each represented by multiple sequence alignments, consensus ... into three broad functional classes: non-coding RNA genes, structured cis-regulatory elements and self ... which may be better preserved than the RNA sequence. The CMs used to describe each ... used by Pfam. CMs can simultaneously model RNA sequence and the structure in an elegant...
  • iRNA-PseColl

  • Referenced in 31 articles [sw24441]
  • PseColl: Identifying the Occurrence Sites of Different RNA Modifications by Incorporating Collective Effects of Nucleotides ... PseKNC. There are many different types of RNA modifications, which are essential for numerous biological ... processes. Knowledge about the occurrence sites of RNA modifications in its sequence ... occurrence sites for several different types of RNA modifications with one seamless package or platform...
  • RegulonDB

  • Referenced in 51 articles [sw25948]
  • v.6.0 now expands beyond transcription initiation, including RNA regulatory elements, specifically riboswitches, attenuators and small...
  • iRNA-AI

  • Referenced in 26 articles [sw24437]
  • adenosine to inosine editing sites in RNA sequences. Catalyzed by adenosine deaminase (ADAR), the adenosine ... inosine (A-to-I) editing in RNA is not only involved in various important biological ... editing sites in RNA is crucially important for both basic research and drug development. Given ... uncharacterized RNA sequence that contains many adenosine (A) residues, can we identify which...
  • 2L-piRNA

  • Referenced in 25 articles [sw27667]
  • interacting RNAs, are of small non-coding RNA with around 19–33 nt in length ... Given a small non-coding RNA molecule, can we predict whether it is of piRNA ... from the other? With the avalanche of RNA sequences emerging in the postgenomic ... layer is for identifying whether a query RNA molecule is piRNA or non-piRNA...
  • PseKNC

  • Referenced in 31 articles [sw22436]
  • used to represent a DNA or RNA sequence with a discrete model or vector ... analysis. However, dealing with different DNA or RNA problems may need different kinds of PseKNC...
  • iRNAm5C-PseDNC

  • Referenced in 23 articles [sw24531]
  • iRNAm5C-PseDNC: identifying RNA 5-methylcytosine sites by incorporating physical-chemical properties into pseudo dinucleotide ... composition. Occurring at cytosine (C) of RNA, 5-methylcytosine (m5C) is an important post-transcriptional ... significant roles in biological processes by regulating RNA metabolism in both eukaryotes and prokaryotes ... other major diseases. Given an uncharacterized RNA sequence that contains many C residues...
  • Mfold

  • Referenced in 42 articles [sw12672]
  • server is to provide easy access to RNA and DNA folding and hybridization software...
  • iRNA-PseU

  • Referenced in 20 articles [sw27659]
  • iRNA-PseU: identifying RNA pseudouridine sites. As the most abundant RNA modification, pseudouridine plays important ... been observed in nearly all kinds of RNA, including transfer RNA, messenger RNA, small nuclear ... nucleolar RNA, and ribosomal RNA. Accordingly, its importance to basic research and drug development ... expensive. Facing the explosive growth of RNA sequences in the postgenomic age, we are challenged...
  • Soap

  • Referenced in 38 articles [sw08915]
  • single-read or pair-end resequencing, small RNA discovery and mRNA tag sequence mapping. SOAP...
  • Prnam-PC

  • Referenced in 18 articles [sw22422]
  • Predicting N(6)-methyladenosine sites in RNA sequences via physical-chemical properties. Just like ... proteins, PTCM (post-transcriptional modification) in RNA plays very important roles in biological processes. Occurring ... most common and abundant PTCMs in RNA found in viruses and most eukaryotes. Given ... uncharacterized RNA sequence containing many GAC motifs, which of them can be methylated, and which...
  • iRNA-3typeA

  • Referenced in 17 articles [sw27660]
  • 3typeA: Identifying Three Types of Modification at RNA’s Adenosine Sites. RNA modifications are additions ... diseases as well. With the avalanche of RNA sequences generated in the post-genomic ... been proposed for identifying various types of RNA modifications one by one. However ... simultaneously identifying several different types of RNA modifications. To address such a challenge, we developed...
  • TopHat

  • Referenced in 23 articles [sw17157]
  • TopHat is a popular spliced aligner for RNA-sequence (RNA-seq) experiments. In this paper...
  • ViennaRNA

  • Referenced in 22 articles [sw10504]
  • programs for the prediction and comparison of RNA secondary structures. RNA secondary structure prediction through...
  • Voom

  • Referenced in 17 articles [sw14009]
  • weights unlock linear model analysis tools for RNA-seq read counts. New normal linear modeling ... presented for analyzing read counts from RNA-seq experiments. The voom method estimates the mean ... Bayes analysis pipeline. This opens access for RNA-seq analysts to a large body ... well or better than count-based RNA-seq methods even when the data are generated...
  • BioProspector

  • Referenced in 29 articles [sw09375]
  • motifs for S. cerevisiae RAP1, B. subtilis RNA polymerase, and E. coli CRP, we have...
  • STAR

  • Referenced in 14 articles [sw02515]
  • STAR: ultrafast universal RNA-seq aligner. Motivation: Accurate alignment of high-throughput RNA-seq data ... throughput of the sequencing technologies. Currently available RNA-seq aligners suffer from high mapping error ... large (>80 billon reads) ENCODE Transcriptome RNA-seq dataset, we developed the Spliced Transcripts Alignment ... STAR) software based on a previously undescribed RNA-seq alignment algorithm that uses sequential maximum...
  • tRNAscan-SE

  • Referenced in 16 articles [sw08005]
  • program for improved detection of transfer RNA genes in genomic sequence. We describe a program ... which identifies 99–100% of transfer RNA genes in DNA sequence while giving less than ... This work represents a practical application of RNA covariance models, which are general, probabilistic secondary...
  • iRNA-Methyl

  • Referenced in 14 articles [sw22439]
  • most abundant modifications in RNA, which plays very important roles in many biological processes ... consuming and expensive. With the avalanche of RNA sequences generated in the postgenomic ... called ”iRNA-Methyl” is proposed by formulating RNA sequences with the ”pseudo dinucleotide composition” into ... which three RNA physiochemical properties were incorporated. Rigorous cross-validation tests have indicated that iRNA...