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The staden sequence analysis package

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Abstract

I describe the current version of the sequence analysis package developed at the MRC Laboratory of Molecular Biology, which has come to be known as the “Staden Package.” The package covers most of the standard sequence analysis tasks such as restriction site searching, translation, pattern searching, comparison, gene finding, and secondary structure prediction, and provides powerful tools for DNA sequence determination. Currently the programs are only available for computers running the UNIX operating system. Detailed information about the package is available from our WWW site: http://www.mrc-lmb.cam.ac.uk/pubseq/.

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References

  1. Staden, R. (1977) Sequence data handling by computer.Nucleic Acids Res. 4, 4037–4051.

    Article  PubMed  CAS  Google Scholar 

  2. Staden, R. (1980) A computer program to search for tRNA genes.Nucleic Acids Res. 8, 817–825.

    Article  PubMed  CAS  Google Scholar 

  3. Staden, R. (1980) A new computer method for the storage and manipulation of DNA gel reading data.Nucleic Acids Res. 8, 3673–3694.

    Article  PubMed  CAS  Google Scholar 

  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.

    Article  PubMed  CAS  Google Scholar 

  5. Staden, R. (1982) An interactive graphics program for comparing and aligning nucleic acid and amino acid sequences.Nucleic Acids Res. 10, 2951–2961.

    Article  PubMed  CAS  Google Scholar 

  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.

    Article  PubMed  CAS  Google Scholar 

  7. Staden, R. (1984) A computer program to enter DNA gel reading data into a computer.Nucleic Acids Res. 12, 499–503.

    Article  PubMed  CAS  Google Scholar 

  8. Staden, R. (1984) Computer methods to locate signals in nucleic acid sequences.Nucleic Acids Res. 12, 505–519.

    Article  PubMed  CAS  Google Scholar 

  9. Staden, R. (1988) Methods to define and locate patterns of motifs in sequences.CABIOS 4, 53–60.

    PubMed  CAS  Google Scholar 

  10. Staden, R. (1989) Methods for discovering novel motifs in nucleic acid sequences.CABIOS 5, 293–298.

    PubMed  CAS  Google Scholar 

  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.

    Article  PubMed  CAS  Google Scholar 

  12. Bonfield, J. K., Smith, K. F., and Staden R. (1995) A new DNA sequence assembly program.Nucleic Acids Res. 23, 4992–4999.

    Article  PubMed  CAS  Google Scholar 

  13. Dear, S. and Staden, R. (1992) A standard file format for data from DNA sequencing instruments.DNA Sequence 3, 107–110.

    Article  PubMed  CAS  Google Scholar 

  14. Bonfield, J. K. and Staden R. Experiment files and their application during large scale sequence projects.DNA Sequence 6, 109–117.

  15. Ousterhout, J. K. (1994)Tcl and the Tk Toolkit. Addison-Wesley, Reading, MA.

    Google Scholar 

  16. Staden, R. (1994) The Staden package, inMethods in Molecular Biology, vol. 25 (Griffin, A. M. and Griffin, H. G., eds.). Humana, Totowa, NJ, pp. 9–170.

    Google Scholar 

  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.

    Article  PubMed  CAS  Google Scholar 

  18. Jurka, J., Walichiewicz, J., and Milosavljevic, A. (1992) Prototypic sequences, for human repetitive DNA.J. Mol. Evolution 35, 286–291.

    Article  CAS  Google Scholar 

  19. Kyte, J. and Doolittle, R. F. (1982) A simple method for displaying the hydropathic character of a protein.J. Mol. Biol. 157, 105–132.

    Article  PubMed  CAS  Google Scholar 

  20. Eisenberg, D., Schwarz, E., Komarony, M., and Wall, R. (1984) Analysis of membrane and surface protein sequences with the hydrophobic moment plot.J. Mol. Biol. 179, 125–142.

    Article  PubMed  CAS  Google Scholar 

  21. Garnier, J., Osguthorpe, D. J., and Robson, B. (1978) Analysis of the accuracy and implications of simple methods for predicting the secondary structure of globular proteins.J. Mol. Biol. 120, 97–120.

    Article  PubMed  CAS  Google Scholar 

  22. Schiffer, M. and Edmundson, A. B. (1967) Use of helical wheels to represent the structures of proteins and to identify the segments with helical potential.Biophys. J. 7, 121–135.

    Article  PubMed  CAS  Google Scholar 

  23. Staden, R. (1985) Computer methods to locate genes and signals in nucleic acid sequences, inGenetic Engineering: Principles and Methods, vol. 7, (Setlow, J. K. and Hollaender, A., eds.), Plenum, New York, pp. 67–114.

    Google Scholar 

  24. Staden, R. (1991) Screening protein and nucleic acid sequences against libraries of patterns.DNA Sequence 1, 369–374.

    Article  PubMed  CAS  Google Scholar 

  25. Staden, R. (1990) Methods to search for patterns in protein and nucleic acid sequences, inMethods in Enzymology, vol. 183 (Doolittle, R. R., ed.), Academic, San Diego, CA, 193–211.

    Google Scholar 

  26. Pearson, W. R. (1994) Using the FASTA program to search protein and DNA sequence databases, inMethods in Molecular Biology, vol. 25: Computer Analysis of Sequence Data, Part II (Griffin, A. M. and Griffin, H. G., eds.), Humana, Totowa, NJ, pp. 9–170.

    Google Scholar 

  27. Gish, W. and States, D. J. (1993). Identification of protein coding regions by database similarity search.Nat. Genet. 3, 266–272.

    Article  PubMed  CAS  Google Scholar 

  28. Staden, R. (1989) Methods for calculating the probabilities of finding patterns in sequences.CABIOS 5, 89–96.

    PubMed  CAS  Google Scholar 

  29. Staden, R. (1990) Finding protein coding regions in genomic sequences, inMethods in Enzymology (Doolittle, R. R., ed.), 183 Academic, San Diego, CA, pp. 163–180.

    Google Scholar 

  30. Fickett, J. W. (1982) Recognition of protein coding regions in DNA sequences.Nucleic Acids Res. 10, 5303–5318.

    Article  PubMed  CAS  Google Scholar 

  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.

    Article  PubMed  CAS  Google Scholar 

  32. McLachlan, A.D. (1971) Test for comparing related amino acid sequences.J. Mol. Biol. 61, 409–424.

    Article  PubMed  CAS  Google Scholar 

  33. Schwartz, R. M. and Dayhoff, M. O. (1978) Matrices for detecting distant relationships, inAtlas of Protein Sequence and Structure, 5 suppl. 3,Nat. Biomed. Res. Found., Washington DC, pp. 353–358.

    Google Scholar 

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Authors and Affiliations

  1. Laboratory of Molecular Biology, Hills Road, CB2 2QH, Cambridge, UK

    Rodger Staden

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  1. Rodger Staden
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Staden, R. The staden sequence analysis package. Mol Biotechnol 5, 233–241 (1996). https://doi.org/10.1007/BF02900361

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  • DOI: https://doi.org/10.1007/BF02900361

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