Depending on the purpose of the analysis, RNA-seq can be performed using different approaches: Ion Torrent sequencing: NGS ... Small RNA sequencing (Small RNA-Seq) is a type of RNA sequencing based on the use of NGS technologies that allows to isolate ... Illumina sequencing: it offers a good method for small RNA sequencing and it is the most widely used approach. After the ... "Small RNA Sequencing , Small RNA and miRNA profiling and discovery". www.illumina.com. Retrieved 2018-11-28. Quail MA, Smith M ...

... spot 42 RNA. I. Nucleotide sequence analysis". J. Mol. Biol. 131 (3): 573-592. doi:10.1016/0022-2836(79)90008-1. PMID 390161. ... Spot 42 (spf) RNA is a regulatory non-coding bacterial small RNA encoded by the spf (spot forty-two) gene. Spf is found in ... Bækkedal, Cecilie; Haugen, Peik (September 2015). "The Spot 42 RNA: A regulatory small RNA with roles in the central metabolism ... Sahagan, Barbara; Dahlberg (5 July 1979). "A small, unstable RNA molecule of Escherichia coli: spot 42 RNA. II. Accumulation ...

An Interactive Online Database for the Analysis of Codon Usage and Sequence Composition". Bioinformatics for DNA Sequence ... it is messenger RNA (mRNA) that directs protein synthesis. The mRNA sequence is determined by the sequence of genomic DNA. In ... In RNA, it is replaced with uracil (U). This is the only difference between the standard RNA codon table and the standard DNA ... In the standard code, the sequence AUG-read as methionine-can serve as a start codon and, along with sequences such as an ...

Eddy SR, Durbin R (June 1994). "RNA sequence analysis using covariance models". Nucleic Acids Research. 22 (11): 2079-88. doi: ... Comparative sequence analysis indicates features typical for mt-tmRNAs. Most conserved is the primary sequence of the amino ... Transfer-messenger RNA (abbreviated tmRNA, also known as 10Sa RNA and by its genetic name SsrA) is a bacterial RNA molecule ... RNA. 3 (1): 89-103. PMC 1369465. PMID 8990402. Zwieb C, Wower I, Wower J (May 1999). "Comparative sequence analysis of tmRNA". ...

Eddy SR, Durbin R (June 1994). "RNA sequence analysis using covariance models". Nucleic Acids Res. 22 (11): 2079-2088. doi: ... 6A RNA motif AbiF RNA motif ARRPOF RNA motif CyVA-1 RNA motif List of RNA structure prediction software Altschul SF, Madden TL ... Homology search refers to the process of searching a sequence database for RNAs that are similar to already known RNA sequences ... Rivas E, Eddy SR (2001). "Noncoding RNA gene detection using comparative sequence analysis". BMC Bioinformatics. 2: 8. doi: ...

Rivas E, Eddy SR (2001). "Noncoding RNA gene detection using comparative sequence analysis". BMC Bioinformatics. 2 (1): 8. doi: ... Eddy SR, Durbin R (June 1994). "RNA sequence analysis using covariance models". Nucleic Acids Research. 22 (11): 2079-2088. doi ... Li AX, Marz M, Qin J, Reidys CM (February 2011). "RNA-RNA interaction prediction based on multiple sequence alignments". ... Busch A, Backofen R (July 2007). "INFO-RNA--a server for fast inverse RNA folding satisfying sequence constraints". Nucleic ...

... and Illumina platform sequencing. These techniques allow analysis of highly complex and heterogeneous RNA populations like ... Piwi-interacting RNA (piRNA) is the largest class of small non-coding RNA molecules expressed in animal cells. piRNAs form RNA- ... 2010). "Virus discovery by deep sequencing and assembly of virus-derived small silencing RNAs". Proc Natl Acad Sci U S A. 107 ( ... Monga I, Banerjee I (November 2019). "Computational Identification of piRNAs Using Features Based on RNA Sequence, Structure, ...

doi:10.1261/rna.1200508. PMC 2590952. PMID 18945806. Alastair Kerr (21 June 2011). "Desktop Sequence Analysis: software review ... "The RNA WikiProject: Community annotation of RNA families". RNA. 14 (12): 2462-2464. ... 2012). "Analysis of Plasmodium falciparum diversity in natural infections by deep sequencing". Nature. 487 (7407): 375-9. ... Manske, H. M.; Kwiatkowski, D. P. (2009). "Look Seq: A browser-based viewer for deep sequencing data". Genome Research. 19 (11 ...

2004). "DNA sequence and analysis of human chromosome 9". Nature. 429 (6990): 369-74. Bibcode:2004Natur.429..369H. doi:10.1038/ ... 2003). "Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences". Proc. Natl. Acad. Sci ... Muth V, Nadaud S, Grummt I, Voit R (2001). "Acetylation of TAF(I)68, a subunit of TIF-IB/SL1, activates RNA polymerase I ... 2006). "Phosphoproteome analysis of the human mitotic spindle". Proc. Natl. Acad. Sci. U.S.A. 103 (14): 5391-6. Bibcode: ...

"High-resolution gene expression profiling for simultaneous kinetic parameter analysis of RNA synthesis and decay". RNA. 14 (9 ... Time-resolved RNA sequencing methods are applications of RNA-seq that allow for observations of RNA abundances over time in a ... as all RNA is run together on the sequencing instrument and labeled RNA is separated from nonlabeled in silico. This reduces ... a researcher can simply sequence the bulk RNA within a sample and measure relative abundances of specific types of RNA by ...

The Arabidopsis Genome Initiative (2000). "Analysis of the genome sequence of the flowering plant Arabidopsis thaliana". Nature ... RNA polymerase IV (RNAP IV) is an enzyme that synthesizes small interfering RNA (siRNA) in plants, which silence gene ... In the first step of heterochromatin formation, RNAP IV couples with an RNA-dependent RNA polymerase known as RDR2 to make a ... Phylogenetic studies of land plants have led to the discovery of RNA Polymerase IV. Analysis of the largest (RPD1) and second- ...

However, northern blot analysis of this 477bp sequence yielded no results. A subsequent tiling array analysis sequencing Hfq- ... FnrS RNA is a family of Hfq-binding small RNA whose expression is upregulated in response to anaerobic conditions. It is named ... "A computational approach to identify genes for functional RNAs in genomic sequences". Nucleic Acids Res. 29 (19): 3928-3938. ... Tjaden B, Saxena RM, Stolyar S, Haynor DR, Kolker E, Rosenow C (September 2002). "Transcriptome analysis of Escherichia coli ...

February 2001). "Initial sequencing and analysis of the human genome". Nature. 409 (6822): 860-921. Bibcode:2001Natur.409..860L ... small interfering RNAs (siRNAs), Piwi-interacting RNAs (piRNAs), small nucleolar RNAs (snoRNAs), and other short RNAs. Given ... indicating at least four times more long non-coding than coding RNA sequences. Large-scale complementary DNA (cDNA) sequencing ... an ncRNA repressor of RNA polymerase II transcription". RNA. 13 (4): 583-596. doi:10.1261/rna.310307. PMC 1831867. PMID ...

In addition to these known EBV ncRNAs, this analysis identified new RNAs, including two stable intronic sequence (sis)RNAs. ... "Genome-wide analyses of Epstein-Barr virus reveal conserved RNA structures and a novel stable intronic sequence RNA". BMC ... "The RNA WikiProject: Community annotation of RNA families". RNA. 14 (12): 2462-2464. doi:10.1261/rna.1200508. PMC 2590952. PMID ... Epstein-Barr virus stable intronic-sequence RNAs (ebv-sisRNAs) are a class of non-coding RNAs generated by repeat introns in ...

Bukh J, Purcell RH, Miller RH (August 1994). "Sequence analysis of the core gene of 14 hepatitis C virus genotypes". ... Negative-sense viral RNA is complementary to mRNA and thus must be converted to positive-sense RNA by an RNA-dependent RNA ... One of these includes RNA-dependent RNA polymerase (RNA replicase), which copies the viral RNA to form a double-stranded ... Very rarely viral RNA can recombine with host RNA. RNA recombination appears to be a major driving force in determining genome ...

2002). "The DNA sequence and comparative analysis of human chromosome 20". Nature. 414 (6866): 865-71. Bibcode:2001Natur.414.. ... 2002). "Purification and characterization of native spliceosomes suitable for three-dimensional structural analysis". RNA. 8 (4 ... 2003). "Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences". Proc. Natl. Acad. Sci ... RNA-binding protein Raly is a protein that in humans is encoded by the RALY gene. In infectious mononucleosis, anti-EBNA-1 ...

Eddy, SR; Durbin, R (11 June 1994). "RNA sequence analysis using covariance models". Nucleic Acids Research. 22 (11): 2079-88. ... In evolutionary biology, conserved sequences are identical or similar sequences in nucleic acids (DNA and RNA) or proteins ... Sequences may also recombine or be deleted due to chromosomal rearrangements. Conserved sequences are sequences which persist ... paralogous sequences), or between donor and receptor taxa (xenologous sequences). Conservation indicates that a sequence has ...

Eddy, S. R.; Durbin, R (1994). "RNA sequence analysis using covariance models". Nucleic Acids Research. 22 (11): 2079-88. doi: ... February 2001). "Initial sequencing and analysis of the human genome" (PDF). Nature. 409 (6822): 860-921. Bibcode:2001Natur.409 ... He has developed numerous methods for computational sequence analysis. These include gene finding (e.g. GeneWise) with Ewan ... A standard textbook Biological Sequence analysis coauthored with Sean Eddy, Anders Krogh and Graeme Mitchison describes some of ...

RseqFlow is an RNA-Seq analysis pipeline which offers an express implementation of analysis steps for RNA sequencing datasets. ... Rail-RNA Scalable analysis of RNA-seq splicing and coverage. RAP RNA-Seq Analysis Pipeline, a new cloud-based NGS web ... Rail-RNA Scalable analysis of RNA-seq splicing and coverage. RPASuite RPASuite (RNA Processing Analysis Suite) is a ... IsoDOT - Differential RNA-isoform Expression. Limma Limma powers differential expression analyses for RNA-sequencing and ...

Shine, John; Dalgarno, Lynne (September 1975). "Terminal‐Sequence Analysis of Bacterial Ribosomal RNA". European Journal of ... This ribosomal binding site in bacterial messenger RNA became known as the Shine-Dalgarno (SD) sequence. It enables initiation ... known as the Shine-Dalgarno sequence) of the ribosome binding site of messenger RNA. - Fyfe Bygrave Shine, John; Dalgarno, Lynn ... "The Shine-Dalgarno sequence - the beginnings of biotechnology , ANU Research School of Biology". biology.anu.edu.au. Retrieved ...

"CummeRbund - An R package for persistent storage, analysis, and visualization of RNA-Seq from cufflinks output". Retrieved 11 ... Bowtie is a software package commonly used for sequence alignment and sequence analysis in bioinformatics. The source code for ... "Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks". Nature Protocols. 7 (3 ... The Bowtie sequence aligner was originally developed by Ben Langmead et al. at the University of Maryland in 2009. The aligner ...

"Sequence analysis of RNase MRP RNA reveals its origination from eukaryotic RNase P RNA". RNA. 12 (5): 699-706. doi:10.1261/rna. ... VegT RNA, Oskar RNA, ENOD40, p53 RNA and SR1 RNA. Bifunctional RNAs have recently been the subject of a special issue of ... A non-coding RNA (ncRNA) is a functional RNA molecule that is not translated into a protein. The DNA sequence from which a ... Ribosomal RNAs catalyse the translation of nucleotide sequences to protein. Another set of ncRNAs, Transfer RNAs, form an ' ...

Meng, J.; Cui, X.; Rao, M. K.; Chen, Y.; Huang, Y. (14 April 2013). "Exome-based analysis for RNA epigenome sequencing data". ... ChIP-sequencing CLIP-Seq DNA Sequencing Valouev A, et al. (September 2008). "Genome-wide analysis of transcription factor ... Peak calling may be conducted on transcriptome/exome as well to RNA epigenome sequencing data from MeRIPseq or m6Aseq for ... It is also possible to do more complex analysis using such tools like combining multiple ChIP-seq signal to detect regulatory ...

RIP-Chip: Similar to ChIP-Seq, but does not employ cross linking methods and utilizes microarray analysis instead of sequencing ... ChiRP-Seq: Measures RNA-bound DNA and proteins. ChIP-exo: Employs exonuclease treatment to achieve up to single base-pair ... ChIL sequencing (ChIL-seq), also known as Chromatin Integration Labeling sequencing, is a method used to analyze protein ... Sequencing of prepared DNA libraries and comparison to whole-genome sequence databases allows researchers to analyze the ...

RIP-Chip: Similar to ChIP-Seq, but does not employ cross linking methods and utilizes microarray analysis instead of sequencing ... ChiRP-Seq: Measures RNA-bound DNA and proteins. ChIP-exo: Employs exonuclease treatment to achieve up to single base-pair ... Sensitivity of sequencing depends on the depth of the sequencing run (i.e. the number of mapped sequence tags), the size of the ... Sequencing of prepared DNA libraries and comparison to whole-genome sequence databases allows researchers to analyze the ...

RIP-Chip: Similar to ChIP-Seq, but does not employ cross linking methods and utilizes microarray analysis instead of sequencing ... ChiRP-Seq: Measures RNA-bound DNA and proteins. ChIP-exo: Employs exonuclease treatment to achieve up to single base-pair ... Sensitivity of sequencing depends on the depth of the sequencing run (i.e. the number of mapped sequence tags), the size of the ... Sequencing of prepared DNA libraries and comparison to whole-genome sequence databases allows researchers to analyze the ...

... is a long non-coding RNA. In humans, it is located on the X chromosome. It was identified during sequence analysis of the X ... 2002). "Comparative sequence analysis of the X-inactivation center region in mouse, human, and bovine". Genome Res. 12 (6): 894 ... Long noncoding RNA "Human PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine ... 2011). "Ftx is a non-coding RNA which affects Xist expression and chromatin structure within the X-inactivation center region ...

January 2015). "Analysis of intron sequences reveals hallmarks of circular RNA biogenesis in animals". Cell Reports. 10 (2): ... sequenced RNA from Archaea. After digesting total RNA with RNase R, they were able to identify circular species, indicating ... Circular RNA (or circRNA) is a type of single-stranded RNA which, unlike linear RNA, forms a covalently closed continuous loop ... RNAs can undergo base modification by RNA editing after transcription. RNA editing occurs mainly in Alu elements of protein- ...

After sequencing RNA-seq analysis can then be performed. Noninvasive method for capturing mRNA from single cells in living, ... This analysis involves characterization of all functional genomic elements, coding and non-coding. The current RNA capture ... Wolf, Jochen B. W. (March 2013). "Principles of transcriptome analysis and gene expression quantification: an RNA-seq tutorial ... The transcriptome is a set of all RNA, including rRNA, mRNA, tRNA, and non-coding RNA. Specifically mRNA transcripts can be ...

RT-PCR, cDNA microarrays, and RNA sequencing are common techniques for RNA analysis. Applying these methods to study exRNAs ... Among these DNA sequencing-derived methods is RNA sequencing. The main advantage of RNA sequencing over other methods for exRNA ... In 2009, Helicos Biosciences published a method for directly sequencing RNA molecules called Direct RNA sequencing (DRS™). ... An RNA sample can then be added to the chip, and RNAs with sequence complementarity to the cDNA probe will bind and generate a ...