Frame: detection of genomic sequencing errors
作者： N. P. Brown , C. Sander , P. Bork
DOI: 10.1093/BIOINFORMATICS/14.4.367
关键词:
摘要: Motivation The underlying error rate for genomic sequencing sometimes results in the introduction of artificial frameshifts and in-frame stop codons into putative protein encoding genes. Severe errors are then introduced inferred transcripts through mis-translation or premature termination. Results We describe a system screening segments DNA frameshift coding regions. method is based on homology matching using blastx to compare all six reading frames query nucleotide sequence against selected databases. Fragments neighbouring regions united extended laterally define candidate open frames, within which, stops identified. Suitable targets include prokaryotic other intron-free complementary DNAs. As an example its use, we report here two frameshifted ORFs that deviate from original TIGR annotations recently released Helicobacter pylori genome. Availability tool accessible via URL http://www.sander.ebi.ac.uk/frame/. Contact brown@ebi.ac.uk.
oup.com
paperity.org参考文章(8)
Peer Bork, Amos Bairoch, Go hunting in sequence databases but watch out for the traps Trends in Genetics. ,vol. 12, pp. 425- 427 ,(1996) , 10.1016/0168-9525(96)60040-7
J. Posfai, R. J. Roberts, Finding errors in DNA sequences. Proceedings of the National Academy of Sciences of the United States of America. ,vol. 89, pp. 4698- 4702 ,(1992) , 10.1073/PNAS.89.10.4698
Stephan Beck, Accuracy of DNA sequencing: Should the sequence quality be monitored? Dna Sequence. ,vol. 4, pp. 215- 217 ,(1993) , 10.3109/10425179309015635
S Altschula, Warren Gisha, Webb Millerb, E Meyersc, D Lipmana, None, Basic Local Alignment Search Tool Journal of Molecular Biology. ,vol. 215, pp. 403- 410 ,(1990) , 10.1016/S0022-2836(05)80360-2
A. Bairoch, R. Apweiler, The SWISS-PROT protein sequence data bank and its supplement TrEMBL Nucleic Acids Research. ,vol. 25, pp. 31- 36 ,(1997) , 10.1093/NAR/25.1.31
David J. States, Molecular sequence accuracy: analysing imperfect data Trends in Genetics. ,vol. 8, pp. 52- 55 ,(1992) , 10.1016/0168-9525(92)90349-9
E. Birney, J. D. Thompson, T. J. Gibson, PairWise and SearchWise: Finding the Optimal Alignment in a Simultaneous Comparison of a Protein Profile against All DNA Translation Frames Nucleic Acids Research. ,vol. 24, pp. 2730- 2739 ,(1996) , 10.1093/NAR/24.14.2730
Xiaojun Guan, Edward C. Uberbacher, Alignments of DNA and protein sequences containing frameshift errors. Bioinformatics. ,vol. 12, pp. 31- 40 ,(1996) , 10.1093/BIOINFORMATICS/12.1.31