• iRNA-PseColl

  • Referenced in 31 articles [sw24441]
  • Identifying the Occurrence Sites of Different RNA Modifications by Incorporating Collective Effects of Nucleotides into ... 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 ... sites for several different types of RNA modifications with one seamless package or platform...
  • iRNA-3typeA

  • Referenced in 17 articles [sw27660]
  • Modification at RNA’s Adenosine Sites. RNA modifications are additions of chemical groups to nucleotides ... 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 ... following three most frequently observed modifications in RNA: (1) N1-methyladenosine (m1A), (2) N6-methyladenosine...
  • iRNA-PseU

  • Referenced in 20 articles [sw27659]
  • pseudouridine sites. As the most abundant RNA modification, pseudouridine plays important roles in many biological ... synthase, the modification has been observed in nearly all kinds of RNA, including transfer...
  • iRNA-2methyl

  • Referenced in 14 articles [sw24530]
  • iRNA-2methyl: Identify RNA 2’-O-methylation Sites by Incorporating Sequence-Coupled Effects into General ... kind of post-transcriptional modification (PTCM) in RNA, the 2’-Omethylation modification occurs ... facing a challenging problem: given an uncharacterized RNA sequence formed by many nucleotides ... methylation modification, and which one cannot? Unfortunately, so far no computational method whatsoever has been...
  • Prnam-PC

  • Referenced in 18 articles [sw22422]
  • modification) in proteins, PTCM (post-transcriptional modification) in RNA plays very important roles in biological...
  • iRNAm5C-PseDNC

  • Referenced in 23 articles [sw24531]
  • RNA, 5-methylcytosine (m5C) is an important post-transcriptional modification (PTCM). The modification plays significant ... other major diseases. Given an uncharacterized RNA sequence that contains many C residues ... them can be of m5C modification, and which one cannot? It is no doubt ... problem, particularly with the explosive growth of RNA sequences in the postgenomic age. Unfortunately...
  • iRNA-Methyl

  • Referenced in 14 articles [sw22439]
  • most abundant modifications in RNA, which plays very important roles in many biological processes...
  • RMBase

  • Referenced in 3 articles [sw27671]
  • resource for decoding the landscape of RNA modifications from high-throughput sequencing data. Although more ... than 100 different types of RNA modifications have been characterized across all living organisms, surprisingly ... developed a novel resource, RMBase (RNA Modification Base, http://mirlab.sysu.edu.cn/rmbase/), to decode the genome ... wide landscape of RNA modifications identified from high-throughput modification data generated by 18 independent...
  • DeepMRMP

  • Referenced in 1 article [sw40011]
  • predictor for multiple types of RNA modification sites using deep learning. RNA modification plays ... role in the regulation of organisms. RNA modification site prediction offers an insight into diverse ... cellular processing. Regarding different types of RNA modification site prediction, it is difficult to tell ... predictor for multiple types of RNA modifications method called DeepMRMP (Multiple Types RNA Modification Sites...
  • iMRM

  • Referenced in 1 article [sw40034]
  • simultaneously identifying multiple kinds of RNA modifications. Motivation: RNA modifications play critical roles ... processes. Knowledge about the distributions of RNA modifications in the transcriptomes will provide clues ... time consuming and laborious for detecting RNA modifications, computational methods have been proposed for this ... superior to existing methods for identifying RNA modifications. Availability and implementation: A user-friendly...
  • BioProspector

  • Referenced in 29 articles [sw09375]
  • prevalent motif patterns in prokaryotes. All these modifications greatly improve the performance of the program ... motifs for S. cerevisiae RAP1, B. subtilis RNA polymerase, and E. coli CRP, we have...
  • RAMPred

  • Referenced in 1 article [sw40019]
  • methyladenosine (m1A) is a prominent RNA modification involved in many biological processes. Accurate identification ... first time. In this method, RNA sequences are encoded by using nucleotide chemical property...
  • BERMP

  • Referenced in 1 article [sw40032]
  • methyladenosine (m6A) is a prevalent RNA methylation modification involved in several biological processes. Hundreds ... integrated approach dubbed as BGRU-based Ensemble RNA Methylation site Predictor (BERMP) has competitive performance...
  • DORAEMON

  • Referenced in 2 articles [sw23314]
  • probabilistic approach. Protein interactions with ribonucleic acids (RNA) are well-known to be crucial ... translation, and post-translational modifications. Identification of the RNA-interacting residues can provide insights into...
  • intePareto

  • Referenced in 1 article [sw41315]
  • analysis of gene expression (RNA-Seq data), and histone modification data for user-defined sets ... level of consistent changes in both RNA-Seq and ChIP-Seq data. Method is described...
  • ModeRNA

  • Referenced in 1 article [sw17142]
  • respective RNA family. ModeRNA can model post-transcriptional modifications, a functionally important feature analogous...
  • SWORD

  • Referenced in 1 article [sw19792]
  • RNA sequences considering their secondary structure. The genetic algorithm with island modification was used ... implementation. The algorithm was applied for searching RNA-motifs interacting with Hu antigen...
  • VARNA

  • Referenced in 5 articles [sw16406]
  • annotation of the secondary structure of RNA, designed as a companion software for web servers ... XFIG). It also allows manual modification and structural annotation of the resulting drawing using either...
  • RNAm5Cfinder

  • Referenced in 1 article [sw40021]
  • RNAm5Cfinder: A Web-server for Predicting RNA 5-methylcytosine (m5C) Sites Based on Random Forest ... methylcytosine (m5C) is a common nucleobase modification, and recent investigations have indicated its prevalence ... server named RNAm5Cfinder based on RNA sequence features and machine learning method to predict...
  • SeqBuster

  • Referenced in 1 article [sw29583]
  • small RNAs datasets, reveals ubiquitous miRNA modifications in human embryonic cells. High-throughput sequencing technologies ... analyze snapshots of the total small RNA content of living cells. Characterization of high-throughput...