ChimeRScope: a novel alignment-free algorithm for fusion transcript prediction using paired-end RNA-Seq data.


:The RNA-Seq technology has revolutionized transcriptome characterization not only by accurately quantifying gene expression, but also by the identification of novel transcripts like chimeric fusion transcripts. The 'fusion' or 'chimeric' transcripts have improved the diagnosis and prognosis of several tumors, and have led to the development of novel therapeutic regimen. The fusion transcript detection is currently accomplished by several software packages, primarily relying on sequence alignment algorithms. The alignment of sequencing reads from fusion transcript loci in cancer genomes can be highly challenging due to the incorrect mapping induced by genomic alterations, thereby limiting the performance of alignment-based fusion transcript detection methods. Here, we developed a novel alignment-free method, ChimeRScope that accurately predicts fusion transcripts based on the gene fingerprint (as k-mers) profiles of the RNA-Seq paired-end reads. Results on published datasets and in-house cancer cell line datasets followed by experimental validations demonstrate that ChimeRScope consistently outperforms other popular methods irrespective of the read lengths and sequencing depth. More importantly, results on our in-house datasets show that ChimeRScope is a better tool that is capable of identifying novel fusion transcripts with potential oncogenic functions. ChimeRScope is accessible as a standalone software at ( or via the Galaxy web-interface at (


Nucleic Acids Res


Nucleic acids research


Li Y,Heavican TB,Vellichirammal NN,Iqbal J,Guda C




Has Abstract


2017-07-27 00:00:00














  • FGF: a web tool for Fishing Gene Family in a whole genome database.

    abstract::Gene duplication is an important process in evolution. The availability of genome sequences of a number of organisms has made it possible to conduct comprehensive searches for duplicated genes enabling informative studies of their evolution. We have established the FGF (Fishing Gene Family) program to efficiently sear...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Zheng H,Shi J,Fang X,Li Y,Vang S,Fan W,Wang J,Zhang Z,Wang W,Kristiansen K,Wang J

    更新日期:2007-07-01 00:00:00

  • Regulation of the androgen receptor by SET9-mediated methylation.

    abstract::The androgen receptor (AR) is a member of the nuclear hormone receptor family of transcription factors that plays a critical role in regulating expression of genes involved in prostate development and transformation. Upon hormone binding, the AR associates with numerous co-regulator proteins that regulate the activati...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Gaughan L,Stockley J,Wang N,McCracken SR,Treumann A,Armstrong K,Shaheen F,Watt K,McEwan IJ,Wang C,Pestell RG,Robson CN

    更新日期:2011-03-01 00:00:00

  • Bidirectional transfer from a 24 bp border repeat of Agrobacterium tumefaciens.

    abstract::T-region transfer from wild-type Agrobacterium strains is thought to be an orientated process, starting at the right border repeat and terminating at the left border repeat of the T-region. Here we demonstrate that a right border repeat in the inverted orientation relative to the onc-genes can also mediate transfer of...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: van Haaren MJ,Sedee NJ,de Boer HA,Schilperoort RA,Hooykaas PJ

    更新日期:1988-11-11 00:00:00

  • Identification of psiB genes of plasmids F and R6-5. Molecular basis for psiB enhanced expression in plasmid R6-5.

    abstract::PsiB protein of plasmid R6-5 inhibits the induction of the SOS pathway. The F sex factor also carries a psiB gene homologous to that of R6-5. Yet, it fails to inhibit SOS induction. In order to solve this difference, we characterized the psiB genes of R6-5 and F. We found that (i) the sequences of the two psiB genes s...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Dutreix M,Bäckman A,Célérier J,Bagdasarian MM,Sommer S,Bailone A,Devoret R,Bagdasarian M

    更新日期:1988-11-25 00:00:00

  • The synthesis of blocked triplet-phosphoramidites and their use in mutagenesis.

    abstract::A general approach for the synthesis of oligonucleotide-triplet phosphoramidites and the synthesis of four such blocks are described. A strategy was devised to minimize the number of dimer precursors needed for synthesis of a complete set of triplet-amidite blocks encoding all 20 amino acids. Whereas synthesis of 20 t...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Ono A,Matsuda A,Zhao J,Santi DV

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  • Mitochondrial membrane-based initial separation of MIWI and MILI functions during pachytene piRNA biogenesis.

    abstract::PIWI-interacting RNAs (piRNAs) engage PIWI proteins to silence transposons and promote germ cell development in animals. In diverse species, piRNA biogenesis occurs near the mitochondrial surface, and involves mitochondrial membrane-anchored factors. In mice, two cytoplasmic PIWI proteins, MIWI and MILI, receive proce...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Ding D,Liu J,Dong K,Melnick AF,Latham KE,Chen C

    更新日期:2019-03-18 00:00:00

  • Deoxyribozymes that recode sequence information.

    abstract::Allosteric nucleic acid ligases have been used previously to transform analyte-binding into the formation of oligonucleotide templates that can be amplified and detected. We have engineered binary deoxyribozyme ligases whose two components are brought together by bridging oligonucleotide effectors. The engineered liga...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Tabor JJ,Levy M,Ellington AD

    更新日期:2006-04-28 00:00:00

  • Elastic properties of ribosomal RNA building blocks: molecular dynamics of the GTPase-associated center rRNA.

    abstract::Explicit solvent molecular dynamics (MD) was used to describe the intrinsic flexibility of the helix 42-44 portion of the 23S rRNA (abbreviated as Kt-42+rGAC; kink-turn 42 and GTPase-associated center rRNA). The bottom part of this molecule consists of alternating rigid and flexible segments. The first flexible segmen...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Rázga F,Koca J,Mokdad A,Sponer J

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  • The fragment structure of a putative HsdR subunit of a type I restriction enzyme from Vibrio vulnificus YJ016: implications for DNA restriction and translocation activity.

    abstract::Among four types of bacterial restriction enzymes that cleave a foreign DNA depending on its methylation status, type I enzymes composed of three subunits are interesting because of their unique DNA cleavage and translocation mechanisms performed by the restriction subunit (HsdR). The elucidated N-terminal fragment st...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Uyen NT,Park SY,Choi JW,Lee HJ,Nishi K,Kim JS

    更新日期:2009-11-01 00:00:00

  • Direct micro-haplotyping by multiple double PCR amplifications of specific alleles (MD-PASA).

    abstract::Analysis of haplotypes is an important tool in population genetics, familial heredity and gene mapping. Determination of haplotypes of multiple single nucleotide polymorphisms (SNPs) or other simple mutations is time consuming and expensive when analyzing large populations, and often requires the help of computational...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Eitan Y,Kashi Y

    更新日期:2002-06-15 00:00:00

  • Human testis expresses a specific poly(A)-binding protein.

    abstract::In testis mRNA stability and translation initiation are extensively under the control of poly(A)-binding proteins (PABP). Here we have cloned a new human testis-specific PABP (PABP3) of 631 amino acids (70.1 kDa) with 92.5% identical residues to the ubiquitous PABP1. A northern blot of multiple human tissues hybridise...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Féral C,Guellaën G,Pawlak A

    更新日期:2001-05-01 00:00:00

  • Air2p is critical for the assembly and RNA-binding of the TRAMP complex and the KOW domain of Mtr4p is crucial for exosome activation.

    abstract::Trf4/5p-Air1/2p-Mtr4p polyadenylation complex (TRAMP) is an essential component of nuclear RNA surveillance in yeast. It recognizes a variety of nuclear transcripts produced by all three RNA polymerases, adds short poly(A) tails to aberrant or unstable RNAs and activates the exosome for their degradation. Despite the ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Holub P,Lalakova J,Cerna H,Pasulka J,Sarazova M,Hrazdilova K,Arce MS,Hobor F,Stefl R,Vanacova S

    更新日期:2012-07-01 00:00:00

  • Impairing the production of ribosomal RNA activates mammalian target of rapamycin complex 1 signalling and downstream translation factors.

    abstract::Ribosome biogenesis is a key process for maintaining protein synthetic capacity in dividing or growing cells, and requires coordinated production of ribosomal proteins and ribosomal RNA (rRNA), including the processing of the latter. Signalling through mammalian target of rapamycin complex 1 (mTORC1) activates all the...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Liu R,Iadevaia V,Averous J,Taylor PM,Zhang Z,Proud CG

    更新日期:2014-04-01 00:00:00

  • Alu retrotransposons promote differentiation of human carcinoma cells through the aryl hydrocarbon receptor.

    abstract::Cell differentiation is a central process in development and in cancer growth and dissemination. OCT4 (POU5F1) and NANOG are essential for cell stemness and pluripotency; yet, the mechanisms that regulate their expression remain largely unknown. Repetitive elements account for almost half of the Human Genome; still, t...

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    authors: Morales-Hernández A,González-Rico FJ,Román AC,Rico-Leo E,Alvarez-Barrientos A,Sánchez L,Macia Á,Heras SR,García-Pérez JL,Merino JM,Fernández-Salguero PM

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  • A nuclear protein with enhanced binding to methylated Sp1 sites in the AIDS virus promoter.

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    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Joel P,Shao W,Pratt K

    更新日期:1993-12-11 00:00:00

  • DNA targeting by Clostridium cellulolyticum CRISPR-Cas9 Type II-C system.

    abstract::Type II CRISPR-Cas9 RNA-guided nucleases are widely used for genome engineering. Type II-A SpCas9 protein from Streptococcus pyogenes is the most investigated and highly used enzyme of its class. Nevertheless, it has some drawbacks, including a relatively big size, imperfect specificity and restriction to DNA targets ...

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    authors: Fedorova I,Arseniev A,Selkova P,Pobegalov G,Goryanin I,Vasileva A,Musharova O,Abramova M,Kazalov M,Zyubko T,Artamonova T,Artamonova D,Shmakov S,Khodorkovskii M,Severinov K

    更新日期:2020-02-28 00:00:00

  • The proofreading exonuclease subunit epsilon of Escherichia coli DNA polymerase III is tethered to the polymerase subunit alpha via a flexible linker.

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    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Ozawa K,Jergic S,Park AY,Dixon NE,Otting G

    更新日期:2008-09-01 00:00:00

  • DNA intercalation without flipping in the specific ThaI-DNA complex.

    abstract::The PD-(D/E)XK type II restriction endonuclease ThaI cuts the target sequence CG/CG with blunt ends. Here, we report the 1.3 Å resolution structure of the enzyme in complex with substrate DNA and a sodium or calcium ion taking the place of a catalytic magnesium ion. The structure identifies Glu54, Asp82 and Lys93 as t...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Firczuk M,Wojciechowski M,Czapinska H,Bochtler M

    更新日期:2011-01-01 00:00:00

  • Nucleotide sequence analysis of the linked left and right hand terminal regions of adenovirus type 5 DNA present in the transformed rat cell line 5RK20.

    abstract::A peculiar phenomenon is observed in several adenovirus type 2 or 5 (Ad2 or Ad5) transformed cell lines: the right hand and left hand terminal regions of the viral genome present in the viral DNA insertions of these cell lines are found to be linked together. A large part of the viral DNA insertion present in the Ad5 ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


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    更新日期:1982-04-10 00:00:00

  • Histone H3 K79 methylation states play distinct roles in UV-induced sister chromatid exchange and cell cycle checkpoint arrest in Saccharomyces cerevisiae.

    abstract::Histone post-translational modifications have been shown to contribute to DNA damage repair. Prior studies have suggested that specific H3K79 methylation states play distinct roles in the response to UV-induced DNA damage. To evaluate these observations, we examined the effect of altered H3K79 methylation patterns on ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Rossodivita AA,Boudoures AL,Mecoli JP,Steenkiste EM,Karl AL,Vines EM,Cole AM,Ansbro MR,Thompson JS

    更新日期:2014-06-01 00:00:00

  • A temperature-sensitive mutant of Escherichia coli affected in the alpha subunit of RNA polymerase.

    abstract::A temperature-sensitive mutant of Escherichia coli affected in the alpha subunit of RNA polymerase has been investigated. Gene mapping and complementation experiments placed the mutation to temperature-sensitivity within the alpha operon at 72 min. on the bacterial chromosome. The rate of RNA synthesis in vivo and the...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Mehrpouyan M,Champney WS

    更新日期:1990-06-25 00:00:00

  • Rice Proteome Database based on two-dimensional polyacrylamide gel electrophoresis: its status in 2003.

    abstract::The Rice Proteome Database is the first detailed database to describe the proteome of rice. The current release contains 21 reference maps based on two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) of proteins from rice tissues and subcellular compartments. These reference maps comprise 11 941 identified pr...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Komatsu S,Kojima K,Suzuki K,Ozaki K,Higo K

    更新日期:2004-01-01 00:00:00

  • Topoisomerase III is essential for accurate nuclear division in Schizosaccharomyces pombe.

    abstract::Topoisomerases catalyse changes in the topological state of DNA and are required for many aspects of DNA metabolism. While the functions of topoisomerases I and II in eukaryotes are well established, the role of topoisomerase III remains poorly defined. We have identified a gene in the fission yeast Schizosaccharomyce...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Goodwin A,Wang SW,Toda T,Norbury C,Hickson ID

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  • Analysis of large nucleic acid dot matrices on small computers.

    abstract::A UCSD Pascal program was developed which can analyze nucleic acid dot matrices of up to 9500 X 9500 in size on the Apple II computer. Although matrices of such size consume large amounts of computer memory, this program minimizes these problems by analyzing only small strips of the matrix at a time, and then transfer...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Zweig SE

    更新日期:1984-01-11 00:00:00

  • Insertion of an LrDNA gene fragment and of filler DNA at a mitochondrial exon-intron junction in Podospora.

    abstract::A rearrangement of the mitochondrial genome of a long lived mutant of Podospora anserina is presented. It consists in the insertion of 191 bp of the LrDNA gene (coding for the large ribosomal RNA) at the junction between exon1 and intron alpha of gene co1 (coding for subunit 1 of cytochrome oxidase). This insertion is...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Sainsard-Chanet A,Begel O

    更新日期:1990-02-25 00:00:00

  • Site-specific DNA binding of nuclear factor I: effect of the spacer region.

    abstract::Nuclear factor I (NFI) is a site-specific DNA binding protein required for the replication of adenovirus type 2 DNA in vitro and in vivo. To study sequence requirements for the interaction of NFI with DNA, we have measured the binding of the protein to a variety of synthetic sites. Binding sites for NFI (FIB sites) we...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Gronostajski RM

    更新日期:1987-07-24 00:00:00

  • p59OASL, a 2'-5' oligoadenylate synthetase like protein: a novel human gene related to the 2'-5' oligoadenylate synthetase family.

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    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Hartmann R,Olsen HS,Widder S,Jorgensen R,Justesen J

    更新日期:1998-09-15 00:00:00

  • High level activity of the mouse CCAAT/enhancer binding protein (C/EBP alpha) gene promoter involves autoregulation and several ubiquitous transcription factors.

    abstract::The promoter region of the mouse CCAAT-Enhancer Binding Protein (C/EBP alpha) gene is capable of directing high levels of expression of reporter constructs in various cell lines, albeit even in cells that do not express their endogenous C/EBP alpha gene. To understand the molecular mechanisms underlying this ubiquitou...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Legraverend C,Antonson P,Flodby P,Xanthopoulos KG

    更新日期:1993-04-25 00:00:00

  • PARN deadenylase is involved in miRNA-dependent degradation of TP53 mRNA in mammalian cells.

    abstract::mRNA deadenylation is under the control of cis-acting regulatory elements, which include AU-rich elements (AREs) and microRNA (miRNA) targeting sites, within the 3' untranslated region (3' UTRs) of eukaryotic mRNAs. Deadenylases promote miRNA-induced mRNA decay through their interaction with miRNA-induced silencing co...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Zhang X,Devany E,Murphy MR,Glazman G,Persaud M,Kleiman FE

    更新日期:2015-12-15 00:00:00

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    abstract::Homo-oligomerization of proteins is abundant in nature, and is often intimately related with the physiological functions of proteins, such as in metabolism, signal transduction or immunity. Information on the homo-oligomer structure is therefore important to obtain a molecular-level understanding of protein functions ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Baek M,Park T,Heo L,Park C,Seok C

    更新日期:2017-07-03 00:00:00