Using the miraEST assembler for reliable and automated mRNA transcript assembly and SNP detection in sequenced ESTs

Genome Research

Volumn 14, Issue 6, 2004, Pages 1147-1159

  Chevreux, Bastien ^a   Pfisterer, Thomas ^b   Drescher, Bernd ^c   Driesel, Albert J ^d   Müller, Werner E G ^e   Wetter, Thomas ^f   Suhai, Sándor ^a  

^a GERMAN CANCER RESEARCH CENTER DKFZ   (Germany)

^b MWG Biotech AG   (Germany)

^c German Genome Resource Center RZPD   (Germany)

^d VitiGen AG   (Germany)

^e JOHANNES GUTENBERG UNIVERSITY   (Germany)

^f UNIVERSITY OF HEIDELBERG   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA;

ARTICLE; AUTOMATION; CELL TYPE; CONTROLLED STUDY; DNA MICROARRAY; DNA TEMPLATE; EXPRESSED SEQUENCE TAG; GENE MUTATION; GENE SEQUENCE; MUTATIONAL ANALYSIS; NONHUMAN; PRIORITY JOURNAL; PROBABILITY; PROTEIN ASSEMBLY; RELIABILITY; RNA TRANSCRIPTION; SENSITIVITY AND SPECIFICITY; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY; SINGLE NUCLEOTIDE POLYMORPHISM;

ANIMALS; BASE PAIRING; BASE SEQUENCE; CHROMOSOME MAPPING; CONTIG MAPPING; DOGS; EXPRESSED SEQUENCE TAGS; MOLECULAR SEQUENCE DATA; POLYMORPHISM, SINGLE NUCLEOTIDE; PORIFERA; RNA, MESSENGER; RNA, PLANT; SEQUENCE ANALYSIS, RNA; SOFTWARE; VITIS;

EID: 3042615882     PISSN: 10889051     EISSN: None     Source Type: Journal    
DOI: 10.1101/gr.1917404     Document Type: Article

References (42)

1. Allex, C.F., Baldwin, S.F., Shavlik, J.W., and Blattner, F.R. 1996. Improving the quality of automatic DNA sequence assembly using fluorescent trace-data classifications. Intell. Systems Mol. Biol. 4: 3-14.
2. Arslan, A.N., Egecioglu, O., and Pevzner, P.A. 2001. A new approach to sequence comparison: Normalized sequence alignment. Bioinformatics 17: 327-337.
3. Baeza-Yates, R.A. and Gonnet, G.H. 1992. A new approach to text searching. Commun. of the Assoc. for Comp. Mach. 35: 74-82.
4. Barker, G., Batley, J., O'Sullivan, H., Edwards, K.J., and Edwards, D. 2003. Redundancy based detection of sequence polymorphisms in expressed sequence tag data using autoSNP. Bioinformatics 19: 421-422.
5. Bonfield, J.K. and Staden, R. 1996. Experiment files and their application during large-scale sequencing projects. DNA Seq. 6: 109-117.
6. Bonfield, J.K., Smith, K.F., and Staden, R. 1995. A new DNA sequence assembly program. Nucleic Acids Res. 23: 4992-4999.
7. Bonfield, J.K., Rada, C., and Staden, R. 1998. Automated detection of point mutations using fluorescent sequence trace subtraction. Nucleic Acids Res. 26: 3404-3409.
8. Camargo, A.A., Samaia, H.P., Dias-Neto, E., Simao, D.F., Migotto, I.A., Briones, M.R., Costa, F.F., Nagai, M.A., Verjovski-Almeida, S., Zago, M.A., et al. 2001. The contribution of 700,000 ORF sequence tags to the definition of the human transcriptome. Proc. Natl. Acad. Sci. 98: 12103-12108.
9. Chan, S.C., Wong, A.K.C., and Chiu, D.K.Y. 1992. A survey of multiple sequence comparison methods. Bull. Mathem. Biol. 54: 563-598.
10. Chevreux, B., Wetter, T., and Suhai, S. 1999. Genome sequence assembly using trace signals and additional sequence information. Comput. Sci. Biol.: Proc. German Conference on Bioinformatics GCB '99 GCB, pp. 45-56.
11. Chevreux, B., Pfisterer, T., and Suhai, S. 2000. Automatic assembly and editing of genomic sequences. In Genomics and proteomics - functional and computational aspects (ed. S. Suhai), Chap. 5, pp. 51-65. Kluwer Academic/Plenum Publishers, New York.
12. Chou, H.-H. and Holmes, M.H. 2001. DNA sequence quality trimming and vector removal. Bioinformatics 17: 1093-1104.
13. Dear, S., Durbin, R., Hilloier, L., Marth, G., Thierry-Mieg, J., and Mott, R. 1998. Sequence assembly with CAFTOOLS. Genome Res. 8: 260-267.
14. Durbin, R. and Dear, S. 1998. Base qualities help sequencing software. Genome Res. 8: 161-162.
15. Giegerich, R. and Wheeler, D. 1996. Pairwise sequence alignment. http://www.techfak.uni-bielefeld.de/bcd/Curric/PrwAli/prwali.html.
16. Grillo, G., Attimonelli, M., Luici, S., and Pesole, G. 1996. CLEANUP: A fast computer program for removing redundancies from nucleotide sequence databases. Comput. Appl. Biosci. 12: 1-8.
17. Gusfield, D. 1997. Algorithms on strings, trees and sequences: Computer science and computational biology. Cambridge University Press, Cambridge, London.
18. Huang, X. 1994. On global sequence alignment. Comput. Appl. Biosci. 10: 227-235.
19. Huang, X. 1996. An improved sequence assembly program. Genomics 33: 21-31.
20. Kececioglu, J.D. and Myers, E.W. 1992. Combinatorial algorithms for DNA sequence assembly. Tech. Rep. TR 92-37, University of California at Davis, University of Arizona, Davis, AZ.
21. Kumar, S. and Rzhetsky, A. 1996. Evolutionary relationships of eukaryotic kingdoms. J. Mol. Evol. 42: 183-193.
22. Morgenstern, B., Dress, A., and Werner, T. 1996. Multiple DNA and protein sequence alignment based on segment-to-segment comparison. Proc. Natl. Acad. Sci. 93: 12098-12103.
23. Müller, W.E. 2001. How was metazoan threshold crossed: The hypothetical Urmetazoa (part A). Compar. Biochem. Physiol. 129: 433-460.
24. Myers, E.W. 1995. Toward simplifying and accurately formulating fragment assembly. J. Computat. Biol. 2: 275-290.
25. Nickerson, D.A., Taylor, S.L., and Rieder, M.J. 2000. Identifying single nucleotide polymorphisms (SNPs) in human candidate genes. In Research abstracts from the DOE human genome program Contractor-Grantee Workshop VIII. Feb. 27 to Mar. 2, 2000. Santa Fe, NM.
26. Notredame, C. and Higgins, D.G. 1996. SAGA: Sequence alignment by genetic algorithm. Nucleic Acids Res. 24: 1515-1524.
27. Paracel 2002a. Paracel filtering package user manual. Paracel, Inc., Pasadena, CA.
28. Paracel 2002b. PTA: Paracel transcript assembler user manual. Paracel, Inc., Pasadena, CA.
29. Parsons, R., Forrest, S., and Burks, C. 1993. Genetic algorithms for DNA sequence assembly. In Proc. of the 1st International Conference on Intelligent Systems for Molecular Biology (eds. L. Hunter et al.). AAAI, Bethesda, MD.
30. Pearson, W.R. 1995. Comparison of methods for searching protein sequence databases. Protein Sci. 4: 1145-1160.
31. Pearson, W.R. 1998. Empirical statistical estimates for sequence similarity searches. J. Mol. Biol. 276: 71-84.
32. Peltola, H., Söderlund, H., and Ukkonen, E. 1984. SEQAID: A DNA sequence assembling program based on a mathematical model. Nucleic Acids Res. 12: 307-321.
33. Pertea, G., Huang, X., Liang, F., Antonescu, V., Sultana, R., Karamycheva, S., Lee, Y., White, J., Cheung, F., Parvizi, B., et al. 2003. TIGR gene indices clustering tools (TGICL): A software system for fast clustering of large EST datasets. Bioinformatics 19: 651-652.
34. Pfisterer, T. and Wetter, T. 1999. Computer assisted editing of genomic sequences - why and how we evaluated a prototype, Lecture Notes in Artificial Intelligence; Subseries of Lecture Notes in Computer Science, pp. 201-209. Springer-Verlag, Berlin, Heidelberg, New York.
35. Shpaer, E.G., Robinson, M., Yee, D., Candlin, J.D., Mines, R., and Hunkapiller, T. 1996. Sensitivity and selectivity in protein similarity searches: Comparison of Smith-Waterman in hardware. Genomics 38: 179-191.
36. Staden, R. 1996. The Staden sequence analysis package. Mol. Biotechnol. 5: 233-241.
37. Staden, R., Bonfield, J., and Beal, K. 1997. The new Staden package manual - 3Part 1. Medical Research Council, Laboratory of Molecular Biology, http://staden.sourceforge.net/.
38. Stoye, J. 1998. Multiple sequence alignment with the divide-and-conquer method. Gene/GC 211: 45-56.
39. Tammi, M.T., Arner, E., Britton, T., and Andersson, B. 2002. Separation of nearly identical repeats in shotgun assemblies using defined nucleotide positions, DNPs. Bioinformatics 18: 379-388.
40. Walther, D., Bartha, G., and Morris, M. 2001. Basecalling with LifeTrace. Genome Res. 11: 875-888.
41. Wu, S. and Manber, U. 1992. Fast text searching allowing errors. Commun. ACM 35: 83-91.
42. Zhang, C. and Wong, A.K. 1997. A genetic algorithm for multiple molecular sequence alignment. Comput. Appl. Biosci. 13: 565-581.