Abstract：
:A crucial step in analyzing mRNA-Seq data is to accurately and efficiently map hundreds of millions of reads to the reference genome and exon junctions. Here we present OLego, an algorithm specifically designed for de novo mapping of spliced mRNA-Seq reads. OLego adopts a multiple-seed-and-extend scheme, and does not rely on a separate external aligner. It achieves high sensitivity of junction detection by strategic searches with small seeds (~14 nt for mammalian genomes). To improve accuracy and resolve ambiguous mapping at junctions, OLego uses a built-in statistical model to score exon junctions by splice-site strength and intron size. Burrows-Wheeler transform is used in multiple steps of the algorithm to efficiently map seeds, locate junctions and identify small exons. OLego is implemented in C++ with fully multithreaded execution, and allows fast processing of large-scale data. We systematically evaluated the performance of OLego in comparison with published tools using both simulated and real data. OLego demonstrated better sensitivity, higher or comparable accuracy and substantially improved speed. OLego also identified hundreds of novel micro-exons (<30 nt) in the mouse transcriptome, many of which are phylogenetically conserved and can be validated experimentally in vivo. OLego is freely available at http://zhanglab.c2b2.columbia.edu/index.php/OLego.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Wu J,Anczuków O,Krainer AR,Zhang MQ,Zhang Cdoi
10.1093/nar/gkt216subject
Has Abstractpub_date
2013-05-01 00:00:00pages
5149-63issue
10eissn
0305-1048issn
1362-4962pii
gkt216journal_volume
41pub_type
杂志文章abstract：:During protein synthesis, the nascent peptide chain traverses the peptide exit tunnel of the ribosome. We monitor the co-translational movement of the nascent peptide using a fluorescent probe attached to the N-terminus of the nascent chain. Due to fluorophore quenching, the time-dependent fluorescence signal emitted ...
journal_title：Nucleic acids research
pub_type： 杂志文章
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abstract：:Stacking self-association equilibria in aqueous solutions of m3uridine, m34,2',3',5'uridine, 2'-deoxyuridine, m13,4,4cytosine, m14,4,4,5cytosine, s2cytidine and s4thymidine were studied at various temperatures by vapour-pressure osmometry. Equilibrium constants Kst's were computed on the assumption of the isodesmic mo...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/3.5.1295
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abstract：:Infrared spectroscopy was used to identify hydration-sensitive structural differences between single- stranded phosphorothioate (PS) and phosphodiester (PO) oligodeoxyribonucleotides. Spectra were recorded in the mid-infrared region, 500-1800 cm-1, at relative humidities between 0 and 98%; the PS and PO spectra are su...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/24.16.3261
更新日期：1996-08-15 00:00:00
abstract：:We have isolated a pigment cell-specific cDNA clone from a B16 mouse melanoma cDNA library by differential hybridization. The mRNA of isolated cDNA is highly expressed in B16 melanoma cells and in black mouse (C57BL/6) skin, but is not detectable in mouse neuroblastoma cells nor in K1735 mouse amelanotic melanoma cell...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/14.6.2413
更新日期：1986-03-25 00:00:00
abstract：:Eight base analogs were tested as third strand residues in otherwise homopyrimidine strands opposite each of the 'direct' (A.T and G.C) and 'inverted' (T.A and C.G) Watson-Crick base pairs, using UV melting profiles to assess triplex stability. The target duplexes contained 20 A.T base pairs and a central test base pa...
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pub_type： 杂志文章
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abstract：:The representational difference analysis (RDA) and other subtraction techniques are used to enrich sample-specific sequences by elimination of ubiquitous sequences existing in both the sample of interest (tester) and the subtraction partner (driver). While applying the RDA to genomic DNA of cutaneous lymphoma cells in...
journal_title：Nucleic acids research
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更新日期：2001-02-15 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/24.14.2841
更新日期：1996-07-15 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
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journal_title：Nucleic acids research
pub_type： 杂志文章
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更新日期：2017-04-07 00:00:00
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journal_title：Nucleic acids research
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更新日期：1976-07-01 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
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更新日期：1983-10-25 00:00:00
abstract：:Mitochondrial DNA (mtDNA) contains high levels of oxidative damage relative to nuclear DNA. A full, functional DNA base excision repair (BER) pathway is present in mitochondria, to repair oxidative DNA lesions. However, little is known about the organization of this pathway within mitochondria. Here, we provide eviden...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gki683
更新日期：2005-07-08 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/16.5.1799
更新日期：1988-03-11 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
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更新日期：1996-11-01 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/20.7.1763
更新日期：1992-04-11 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkx439
更新日期：2017-07-03 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkl136
更新日期：2006-04-20 00:00:00
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journal_title：Nucleic acids research
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更新日期：2012-07-01 00:00:00
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更新日期：1998-09-15 00:00:00
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journal_title：Nucleic acids research
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journal_title：Nucleic acids research
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更新日期：1990-02-25 00:00:00
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journal_title：Nucleic acids research
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journal_title：Nucleic acids research
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更新日期：2020-03-18 00:00:00
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journal_title：Nucleic acids research
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更新日期：1995-09-25 00:00:00
abstract：:The 5'-flanking region of the bovine prolactin gene was cloned and sequenced. The expression of chimeric gene constructs containing 5'-flanking DNA fragments from the prolactin gene joined to a reporter gene encoding human growth hormone (hGH) was examined using transiently transfected rat pituitary cells. Prolactin n...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：
更新日期：1990-08-25 00:00:00
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journal_title：Nucleic acids research
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journal_title：Nucleic acids research
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更新日期：2012-02-01 00:00:00
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journal_title：Nucleic acids research
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更新日期：2017-01-25 00:00:00
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journal_title：Nucleic acids research
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更新日期：2010-09-01 00:00:00
