Copyright (C) 1999-2002, Medical Research Council, Laboratory of Molecular Biology.

Publications

1. Bonfield, James K. and Staden, Rodger. ZTR: a new format for DNA sequence trace data. Bioinformatics 18, 3-10, (2002).
2. Bonfield, James, K., Beal, Kathryn F., Betts, Matthew J. and Staden, Rodger. Trev: a DNA trace editor and viewer. Bioinformatics 18, 194-195, (2002)
3. Rodger Staden, David P. Judge and James K. Bonfield Sequence assembly and finishing methods Bioinformatics. A Practical Guide to the Analysis of Genes and Proteins. Second Edition Eds. Andreas D. Baxevanis and B. F. Francis Ouellette. John Wiley & Sons, New York, NY, USA, (2001)
4. The C. elegans Sequencing Consortium. Genome Sequence of the Nematode C. elegans: A Platform for Investigating Biology. Science 282, 2012-2018 (1998)
5. Rodger Staden, Kathryn F. Beal and James K. Bonfield The Staden Package, 1998. Computer Methods in Molecular Biology Eds Stephen Misener and Steve Krawetz. The Humana Press Inc., Totowa, NJ 07512
6. Bonfield, J.K., Rada, C. and Staden, R. Automated detection of point mutations using flourescent sequence trace subtraction. Nucleic Acids Res. 26, 3404-3409 (1998)
7. Flint, J., Sims, M., Clark, K., Staden, R. and Thomas, K. An Oligo-Screening Strategy to Fill Gaps Found During Shotgun Sequencing Projects. DNA Sequence 8, 241-245 (1998)
8. Staden, R. The Staden Sequence Analysis Package. Molecular Biotechnology 5, 233-241 (1996)
9. Bonfield, J.K. and Staden, R. Experiment files and their application during large-scale sequencing projects. DNA Sequence 6, 109-117 (1996)
10. Staden, R. Indexing and using sequence databases. Methods in Enzymology 266, 105-114 (1996)
11. Bonfield, J.K., Smith, K.F. and Staden, R. A new DNA sequence assembly program. Nucleic Acids Res. 24, 4992-4999 (1995)
12. Bonfield, J.K. and Staden, R. The application of numerical estimates of base calling accuracy to DNA sequencing projects. Nucleic Acids Res. 23, 1406-1410 (1995)
13. Dear, S. and Staden, R. A standard file format for data from DNA sequencing instruments. DNA Sequence 3, 107-110 (1992)
14. Staden, R. and Dear, S. Indexing the sequence libraries: Software providing a common indexing system for all the standard sequence libraries. DNA Sequence 3, 99-105 (1992).
15. Dear, S. and Staden, R. A sequence assembly and editing program for efficient management of large projects. Nucleic Acid Res. 19, 3907-3911 (1991).
16. Staden, R. Screening protein and nucleic acid sequences against libraries of patterns. DNA Sequence 1, 369-374 (1991).
17. Staden, R. Searching for patterns in protein and nucleic acid sequences. Methods in Enzymology 183, 193-211. (1990).
18. Staden, R. Finding protein coding regions in genomic sequences. Methods in Enzymology 183, 163-180. (1990).
19. Staden, R. Methods for discovering novel motifs in nucleic acid sequences. CABIOS 5, 293-298 (1989)
20. Staden R, Methods for calculating the probabilities of finding patterns in sequences. CABIOS 5 89-96 (1989)
21. Staden R, Methods to define and locate patterns of motifs in sequences. CABIOS 4, 53-60 (1988)
22. Staden, R. Graphic methods to determine the function of nucleic acid sequences. Nucleic Acid Res. 12, 521-538 (1984)
23. Staden, R. Computer methods to locate signals in nucleic acid sequences. Nucleic Acid Res. 12, 505-519 (1984)
24. Staden, R. A computer program to enter DNA gel reading data into a computer. Nucleic Acid Res. 12, 499-503 (1984)
25. Staden, R. Measurements of the effects that coding for a protein has on a DNA sequence and their use for finding genes. Nucleic Acid Res. 12, 551-567 (1984)
26. Staden, R. and McLachlan, A.D. Codon preference and its use in identifying protein coding regions in long DNA sequences. Nucleic Acid Res. 10 141-156 (1982)
27. Staden, R. Automation of the computer handling of gel reading data produced by the shotgun method of DNA sequencing. Nucleic Acid Res. 10, 4731-4751 (1982)
28. Staden, R. An interactive graphics program for comparing and aligning nucleic acid and amino acid sequences. Nucleic Acid Res. 10, 2951-2961 (1982)
29. Staden, R. A new computer method for the storage and manipulation of DNA gel reading data. Nucleic Acid Res. 8, 3673-3694 (1980)
30. Staden, R. A computer program to search for tRNA genes. Nucleic Acid Res. 8, 817-825 (1980)