• Rfam

  • Referenced in 33 articles [sw04637]
  • collection of RNA families, each represented by multiple sequence alignments, consensus secondary structures and covariance ... into three broad functional classes: non-coding RNA genes, structured cis-regulatory elements and self ... better preserved than the RNA sequence. The CMs used to describe each family ... Pfam. CMs can simultaneously model RNA sequence and the structure in an elegant and accurate...
  • iRNA-AI

  • Referenced in 26 articles [sw24437]
  • adenosine to inosine editing sites in RNA sequences. Catalyzed by adenosine deaminase (ADAR), the adenosine ... drug development. Given an uncharacterized RNA sequence that contains many adenosine (A) residues ... important problem based on the RNA sequence information alone. To fill this empty area ... sliding occurrence density distribution along a RNA sequence into the general form of pseudo nucleotide...
  • Pse-in-One

  • Referenced in 41 articles [sw22407]
  • pseudo components of DNA, RNA, and protein sequences. With the avalanche of biological sequences generated ... effectively formulate the sequence of a biological sample (such as DNA, RNA or protein) with ... vector that can effectively reflect its sequence pattern information or capture its key features concerned ... possible feature vectors for DNA, RNA and protein sequences. Particularly, it can also generate those...
  • PseKNC

  • Referenced in 31 articles [sw22436]
  • used to represent a DNA or RNA sequence with a discrete model or vector ... genomics and genome sequence analysis. However, dealing with different DNA or RNA problems may need ... useful tool in computational genomics and genome sequence analysis...
  • iRNAm5C-PseDNC

  • Referenced in 23 articles [sw24531]
  • other major diseases. Given an uncharacterized RNA sequence that contains many C residues ... particularly with the explosive growth of RNA sequences in the postgenomic age. Unfortunately...
  • Prnam-PC

  • Referenced in 18 articles [sw22422]
  • Predicting N(6)-methyladenosine sites in RNA sequences via physical-chemical properties. Just like ... most eukaryotes. Given an uncharacterized RNA sequence containing many GAC motifs, which of them ... problem. Particularly with the avalanche of RNA sequences generated in the postgenomic ... predictor called pRNAm-PC, in which RNA sequence samples are expressed by a novel mode...
  • TopHat

  • Referenced in 23 articles [sw17157]
  • popular spliced aligner for RNA-sequence (RNA-seq) experiments. In this paper, we describe TopHat2 ... various lengths produced by the latest sequencing technologies, while allowing for variable-length indels with...
  • iRNA-PseU

  • Referenced in 20 articles [sw27659]
  • expensive. Facing the explosive growth of RNA sequences in the postgenomic age, we are challenged ... computational approaches: For an uncharacterized RNA sequence, can we predict which of its uridine sites...
  • 2L-piRNA

  • Referenced in 25 articles [sw27667]
  • RNA molecule, can we predict whether it is of piRNA according to its sequence information ... other? With the avalanche of RNA sequences emerging in the postgenomic age, it is urgent ... layer is for identifying whether a query RNA molecule is piRNA or non-piRNA...
  • iRNA-3typeA

  • Referenced in 17 articles [sw27660]
  • well. With the avalanche of RNA sequences generated in the post-genomic age, many computational ... been proposed for identifying various types of RNA modifications one by one. However ... rigorous cross-validations for the RNA sequences from Homo sapiens and Mus musculus transcriptomes that...
  • 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 ... challenging problem: given an uncharacterized RNA sequence formed by many nucleotides of A (adenine ... along the RNA sequence concerned, respectively. RESULTS: Rigorous jackknife cross-validations have indicated that...
  • iRNA-Methyl

  • Referenced in 14 articles [sw22439]
  • expensive. With the avalanche of RNA sequences generated in the postgenomic age, it is highly ... iRNA-Methyl” is proposed by formulating RNA sequences with the ”pseudo dinucleotide composition” into which...
  • RSEARCH

  • Referenced in 10 articles [sw23815]
  • RSEARCH: finding homologs of single structured RNA sequences. BACKGROUND: For many RNA molecules, secondary structure ... program, RSEARCH, that takes a single RNA sequence with its secondary structure and utilizes ... single nucleotide substitution matrices for RNA sequences called RIBOSUM matrices. RSEARCH reports the statistical confidence ... programs in finding homologs of structured RNA sequences...
  • STAR

  • Referenced in 14 articles [sw02515]
  • aligner. Motivation: Accurate alignment of high-throughput RNA-seq data is a challenging ... constantly increasing throughput of the sequencing technologies. Currently available RNA-seq aligners suffer from high ... also capable of mapping full-length RNA sequences. Using Roche 454 sequencing of reverse transcription...
  • iRNA-PseColl

  • Referenced in 31 articles [sw24441]
  • 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 ... sequence elements into the general pseudo K-tuple nucleotide composition (PseKNC) of RNA...
  • iMiRNA-PseDPC

  • Referenced in 10 articles [sw22425]
  • microRNA (miRNA) is a small non-coding RNA molecule, functioning in transcriptional and post-transcriptional ... from the false ones (such as hairpin sequences with similar stem ... loops). Particularly, with the avalanche of RNA sequences generated in the post-genomic ... called ”iMiRNA-PseDPC”, in which the RNA sequences are formulated by a novel feature vector...
  • Pfold

  • Referenced in 12 articles [sw23813]
  • available programs for RNA secondary structure prediction only use a single sequence at a time ... possible to obtain related RNA sequences with conserved secondary structure. These should be included ... predicting RNA secondary structure that is especially useful when related sequences can be obtained...
  • Soap

  • Referenced in 38 articles [sw08915]
  • sequencing using the new generation Illumina-Solexa sequencing technology. SOAP is compatible with numerous applications ... pair-end resequencing, small RNA discovery and mRNA tag sequence mapping. SOAP is a command...
  • DEGseq

  • Referenced in 11 articles [sw07998]
  • from RNA-seq data. High-throughput RNA sequencing (RNA-seq) is rapidly emerging...
  • RNAlign

  • Referenced in 7 articles [sw33856]
  • RNAlign Program: Alignment of RNA Sequences Using Both Primary and Secondary Structures. We have developed ... computer program for aligning new RNA sequences with a bank of aligned homologous RNA sequences ... aligned with possible stems in the new sequence. The algorithm has been implemented in Turbo ... been used to align RNA sequences of eubacterial large ribosomal subunit...