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| 1 | Comparative analysis of de novo transcriptome assembly显示文摘The fast development of next-generation sequencing technology presents a major computational challenge for data processing and analysis.A fast algorithm,de Bruijn graph has been successfully used for genome DNA de novo assembly;nevertheless,its performance for transcriptome assembly is unclear.In this study,we used both simulated and real RNA-Seq data,from either artificial RNA templates or human transcripts,to evaluate five de novo assemblers,ABySS,Mira,Trinity,Velvet and Oases.Of these assemblers,ABySS,Trinity,Velvet and Oases are all based on de Bruijn graph,and Mira uses an overlap graph algorithm.Various numbers of RNA short reads were selected from the External RNA Control Consortium(ERCC) data and human chromosome 22.A number of statistics were then calculated for the resulting contigs from each assembler.Each experiment was repeated multiple times to obtain the mean statistics and standard error estimate.Trinity had relative good performance for both ERCC and human data,but it may not consistently generate full length transcripts.ABySS was the fastest method but its assembly quality was low.Mira gave a good rate for mapping its contigs onto human chromosome 22,but its computational speed is not satisfactory.Our results suggest that transcript assembly remains a challenge problem for bioinformatics society.Therefore,a novel assembler is in need for assembling transcriptome data generated by next generation sequencing technique. | CLARKE Kaitlin YANG Yi MARSH Ronald XIE LingLin ZHANG Ke K. | 2013 | Science China(Life Sciences)2013，56，2： | 3 |
| 2 | Esophageal perforation following anterior cervical spine surgery显示文摘 | Newhouse KE Lindesy RW Clark CR | 1989 | Spine1989，14，： | 1 |
| 3 | Low serura vitamin D levels and tuberculo- sis: a systematic review and metz-analysis 显示文摘 | Nnoabam KE Clarke A | 2008 | Int J Epidemiol2008，37，1： | 1 |
| 4 | Low serum vitamin D levels and tubercu-losis : a systematic review and recta-analysis 显示文摘 | Nnoahmn KE Clarke A | 2008 | Im J Epidemiol2008，37，1： | 1 |
| 5 | Transcription factors and congenital heart defects显示文摘 | Clark KL Yutzey KE Benson DW | 2006 | Annu Rev Physiol2006，68，： | 1 |
| 6 | Low serum vitamin D levels and tuberculosis: a systematic review and recta-analysis显示文摘 | Nnoaham KE Clarke A | 2008 | Int J Epidemio12008，37，1： | 1 |
| 7 | Transcription factors and congenital heart defects 显示文摘 | Clark KL Yutzey KE Benson DW | 2006 | Annu Rev Physiol2006，68，： | 1 |
| 8 | CYP3A4 drug interactions: correlation of 10 in vitro probe substrates显示文摘 | KENWORTHY KE BLOOMER JC CLARKE SE | 1999 | Br J Clin Pharmacol1999，48，5： | 1 |
| 9 | Transcription factors and congenital heart defects 显示文摘 | Clark KL Yutzey KE Benson DW | 2006 | Annu Rev Physiol2006，68，： | 1 |
| 10 | Changes in fetal ovine me- tabolism and oxygen delivery with fetal bypass 显示文摘 | Lam CT Baker RS Clark KE | 2011 | Am J Physiol Regul Integr Comp Physiol2011，301，1： | 1 |
| 11 | Divergent transcriptomic responses to repeated and single cold exposures in Drosophila melanogaster显示文摘 | Zhang J Marshall KE Westwood JT Clark MS Sinclair BJ | | 0，，23： | 1 |
| 12 | Transcription factors and congenital heart defects显示文摘 | Clark KL Yutzey KE Benson DW | 2006 | Annu Rev Physiol2006，68，： | 1 |
| 13 | Transcription factors and congenital heart defects显示文摘 | Clark KL Yutzey KE Benson DW | 2006 | Annu Rev Physiol2006，68，： | 1 |
| 14 | CYP3A4 drug interactions:correlation of 10 invitro probe substrates显示文摘 | Kenworthy KE Bloomer JC Clarke SE | 1999 | Br J Clin Pharmacol1999，48，5： | 1 |
| 15 | The MIF antagonist ISO-1 attenuates corticosteroid-insensitive inflammation and airways hyperresponsiveness in an ozone-induced model of COPD显示文摘 | RUSSELL KE CHUNG KF CLARKE CJ | 2016 | PLoS One2016，11，01： | 1 |
| 16 | Low serum vitamin D levels and tuberculosis:a systematic review and meta-analysis显示文摘 | Nnoaham KE Clarke A | | 0，，1： | 1 |
| 17 | Transcription factors and congenital heart defects显示文摘 | Clark KL Yutzey KE Benson DW | 2006 | Annu Rev Physio12006，68，： | 1 |
| 18 | Transcription factors and congenital heart defects 显示文摘 | Clark KL Yutzey KE Benson DW | 2006 | Annu Rev Physiol2006，68，2： | 1 |
| 19 | Reoperative thyroid surgery显示文摘 | Levin KE Clark AH Duh QY | 1999 | Surgery1999，126，34： | 1 |
| 20 | Age-related permeability changes in rabbit corneas显示文摘 | Clark AF Gracy RW | 1999 | Ocul Pharmacol Ther1999，15，6： | 1 |
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