Transcript mapping based on dRNA-seq data

BMC Bioinformatics

Volumn 15, Issue 1, 2014, Pages

  Bischler, Thorsten ^a,b   Kopf, Matthias ^a   Voß, Björn ^a  

^a UNIVERSITY OF FREIBURG   (Germany)

^b UNIVERSITY OF WÜRZBURG   (Germany)

Author keywords

Differential RNA seq; Dynamic programming; RNA seq; Segmentation; Transcriptional start site; Transcriptional unit; Transcriptome

Indexed keywords

ALGORITHMS; DYNAMIC PROGRAMMING; GENES; IMAGE SEGMENTATION; TRANSCRIPTION;

DIFFERENTIAL RNA-SEQ; RNA-SEQ; TRANSCRIPTIONAL START SITE; TRANSCRIPTIONAL UNITS; TRANSCRIPTOMES;

RNA;

BACTERIA (MICROORGANISMS); HELICOBACTER; PROKARYOTA;

ALGORITHM; ARTICLE; GENE EXPRESSION PROFILING; GENETICS; GENOMICS; HELICOBACTER PYLORI; METHODOLOGY; OPERON; SEQUENCE ANALYSIS; TRANSCRIPTION INITIATION SITE; UNTRANSLATED REGION;

ALGORITHMS; GENE EXPRESSION PROFILING; GENOMICS; HELICOBACTER PYLORI; OPERON; SEQUENCE ANALYSIS, RNA; TRANSCRIPTION INITIATION SITE; UNTRANSLATED REGIONS;

EID: 84900330493     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-15-122     Document Type: Article

References (19)

1. Wang Z, Gerstein M, Snyder M. RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet 2009, 10:57-63. 10.1038/nrg2484, 2949280, 19015660.
2. Sharma CM, Hoffmann S, Darfeuille F, Reignier J, Sittka SFA, Chabas S, Reiche K, Hackermüller J, Reinhardt R, Stadler PF, Vogel J. The primary transcriptome of the major human pathogen Helicobacter pylori. Nature 2010, 464(7286):250-255. 10.1038/nature08756, 20164839.
3. Huber W, Toedling J, Steinmetz LM. Transcript mapping with high-density oligonucleotide tiling arrays. Bioinformatics 2006, 22(16):1963-1970. 10.1093/bioinformatics/btl289, 16787969.
4. Nicolas P, Leduc A, Robin S, Rasmussen S, Jarmer H, Bessières P. Transcriptional landscape estimation from tiling array data using a model of signal shift and drift. Bioinformatics 2009, 25(18):2341-2347. 10.1093/bioinformatics/btp395, 2735659, 19561016.
5. Roberts A, Pimentel H, Trapnell C, Pachter L. Identification of novel transcripts in annotated genomes using RNA-Seq. Bioinformatics 2011, 27(17):2325-2329. 10.1093/bioinformatics/btr355, 21697122.
6. Guttman M, Garber M, Levin JZ, Donaghey J, Robinson J, Adiconis X, Fan L, Koziol MJ, Gnirke A, Nusbaum C, Rinn JL, Lander ES, Regev A. Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs. Nat Biotechnol 2010, 28(5):503-510. 10.1038/nbt.1633, 2868100, 20436462.
7. Birol I, Jackman SD, Nielsen CB, Qian JQ, Varhol R, Stazyk G, Morin RD, Zhao Y, Hirst M, Schein JE, Horsman DE, Connors JM, Gascoyne RD, Marra MA, Jones SJM. De novo transcriptome assembly with ABySS. Bioinformatics 2009, 25(21):2872-2877. 10.1093/bioinformatics/btp367, 19528083.
8. Li R, Yu C, Li Y, Lam T, Yiu S, Kristiansen K, Wang J. SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics 2009, 25(15):1966-1967. 10.1093/bioinformatics/btp336, 19497933.
9. Hoffmann S, Otto C, Kurtz S, Sharma CM, Khaitovich P, Vogel J, Stadler PF, Hackermüller J. Fast mapping of short sequences with mismatches, insertions and deletions using index structures. PLoS Comput Biol 2009, 5(9):e1000502. 10.1371/journal.pcbi.1000502, 2730575, 19750212.
10. Rutherford K, Parkhill J, Crook J, Horsnell T, Rice P, Rajandream M, Barrell B. Artemis: sequence visualization and annotation. Bioinformatics 2000, 16:944-945. 10.1093/bioinformatics/16.10.944, 11120685.
11. Mao F, Dam P, Chou J, Olman V, Xu Y. DOOR: a database for prokaryotic operons. Nucl Acids Res 2009, 37:D459-D463. 10.1093/nar/gkn757, 2686520, 18988623.
12. Li W. RNASeqReadSimulator. 2013, [https://github.com/davidliwei/RNASeqReadSimulator].
13. Mitschke J, Georg J, Scholz I, Sharma CM, Dienst D, Bantscheff J, Voß B, Steglich C, Wilde A, Vogel J, Hess WR. An experimentally anchored map of transcriptional start sites in the model cyanobacterium Synechocystis sp. PCC6803. Proc Natl Acad Sci U S A 2011, 108(5):2124-2129. 10.1073/pnas.1015154108, 3033270, 21245330.
14. Landick R. RNA polymerase slides home: pause and termination site recognition. Cell 1997, 88(6):741-744. 10.1016/S0092-8674(00)81919-4, 9118216.
15. Lesnik EA, Sampath R, Levene HB, Henderson TJ, McNeil JA, Ecker DJ. Prediction of rho-independent transcriptional terminators in Escherichia coli. Nucleic Acids Res 2001, 29(17):3583-3594. 10.1093/nar/29.17.3583, 55870, 11522828.
16. Vijayan V, Jain IH, O'Shea EK. A high resolution map of a cyanobacterial transcriptome. Genome Biol 2011, 12(5):R47. 10.1186/gb-2011-12-5-r47, 3219970, 21612627.
17. Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, Salzberg SL, Wold BJ, Pachter L. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol 2010, 28(5):511-515. 10.1038/nbt.1621, 3146043, 20436464.
18. Trapnell C. Can i use cufflinks with RNA-Seq data from bacteria?. 2014, [http://cufflinks.cbcb.umd.edu/faq.html#bact].
19. Schmidtke C, Findeiß S, Sharma CM, Kuhfuß J, Hoffmann S, Vogel J, Stadler PF, Bonas U. Genome-wide transcriptome analysis of the plant pathogen Xanthomonas identifies sRNAs with putative virulence functions. Nucleic Acids Res 2012, 40(5):2020-2031. 10.1093/nar/gkr904, 3300014, 22080557.