The Staden Sequence Analysis Package

Applied Biochemistry and Biotechnology - Part B Molecular Biotechnology

Volumn 5, Issue 3, 1996, Pages 233-241

  Staden, Rodger ^a  

^a MRC LABORATORY OF MOLECULAR BIOLOGY   (United Kingdom)

Author keywords

Gene finding, motif searching; SCF files; Sequence analysis, sequence comparison; Sequence assembly

Indexed keywords

DATA BASE; GENE LIBRARY; MOLECULAR GENETICS; REVIEW; SEQUENCE ALIGNMENT;

DATABASE MANAGEMENT SYSTEMS; GENOMIC LIBRARY; MOLECULAR SEQUENCE DATA; SEQUENCE ALIGNMENT;

EID: 0030158571     PISSN: 10736085     EISSN: None     Source Type: Journal    
DOI: 10.1007/BF02900361     Document Type: Review

References (33)

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2. Staden, R. (1980) A computer program to search for tRNA genes. Nucleic Acids Res. 8, 817-825.
3. Staden, R. (1980) A new computer method for the storage and manipulation of DNA gel reading data. Nucleic Acids Res. 8, 3673-3694.
4. Staden, R. and McLachlan, A. D. (1982) Codon preference and its use in identifying protein coding regions in long DNA sequences. Nucleic Acids Res. 10, 141-156.
5. Staden, R. (1982) An interactive graphics program for comparing and aligning nucleic acid and amino acid sequences. Nucleic Acids Res. 10, 2951-2961.
6. Staden, R. (1982) Automation of the computer handling of gel reading data produced by the shotgun method of DNA sequencing. Nucleic Acids Res. 10, 4731-4751.
7. Staden, R. (1984) A computer program to enter DNA gel reading data into a computer. Nucleic Acids Res. 12, 499-503.
8. Staden, R. (1984) Computer methods to locate signals in nucleic acid sequences. Nucleic Acids Res. 12, 505-519.
9. Staden, R. (1988) Methods to define and locate patterns of motifs in sequences. CABIOS 4, 53-60.
10. Staden, R, (1989) Methods for discovering novel motifs in nucleic acid sequences. CABIOS 5, 293-298.
11. Staden, R. and Dear, S. (1992) Indexing the sequence libraries: software providing a common indexing system for all the standard sequence libraries. DNA Sequence 3, 99-105.
12. Bonfield J. K., Smith, K. F., and Staden R. (1995) A new DNA sequence assembly program. Nucleic Acids Res. 23, 4992-4999.
13. Dear, S. and Staden, R. (1992) A standard file format for data from DNA sequencing instruments. DNA Sequence 3, 107-110.
14. Bonfield, J. K. and Staden R. Experiment files and their application during large scale sequence projects. DNA Sequence 6, 109-117.
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17. Bonfield, J. K and Staden, R. (1995) The application of numerical estimates of base calling accuracy to DNA sequencing projects. Nucleic Acids Res. 23, 1406-1410.
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24. Staden, R. (1991) Screening protein and nucleic acid sequences against libraries of patterns. DNA Sequence 1, 369-374.
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27. Gish, W. and States, D. J. (1993). Identification of protein coding regions by database similarity search. Nat. Genet. 3, 266-272.
28. Staden, R. (1989) Methods for calculating the probabilities of finding patterns in sequences. CABIOS 5, 89-96.
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31. Staden, R. (1984) Measurements of the effects that coding for a protein has on on a DNA sequence and their use for finding genes. Nucleic Acids Res. 12, 551-567.
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