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
Staden, R. (1977) Sequence data handling by computer.Nucleic Acids Res. 4, 4037–4051.
Staden, R. (1980) A computer program to search for tRNA genes.Nucleic Acids Res. 8, 817–825.
Staden, R. (1980) A new computer method for the storage and manipulation of DNA gel reading data.Nucleic Acids Res. 8, 3673–3694.
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.
Staden, R. (1982) An interactive graphics program for comparing and aligning nucleic acid and amino acid sequences.Nucleic Acids Res. 10, 2951–2961.
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.
Staden, R. (1984) A computer program to enter DNA gel reading data into a computer.Nucleic Acids Res. 12, 499–503.
Staden, R. (1984) Computer methods to locate signals in nucleic acid sequences.Nucleic Acids Res. 12, 505–519.
Staden, R. (1988) Methods to define and locate patterns of motifs in sequences.CABIOS 4, 53–60.
Staden, R. (1989) Methods for discovering novel motifs in nucleic acid sequences.CABIOS 5, 293–298.
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.
Bonfield, J. K., Smith, K. F., and Staden R. (1995) A new DNA sequence assembly program.Nucleic Acids Res. 23, 4992–4999.
Dear, S. and Staden, R. (1992) A standard file format for data from DNA sequencing instruments.DNA Sequence 3, 107–110.
Bonfield, J. K. and Staden R. Experiment files and their application during large scale sequence projects.DNA Sequence 6, 109–117.
Ousterhout, J. K. (1994)Tcl and the Tk Toolkit. Addison-Wesley, Reading, MA.
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.
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.
Jurka, J., Walichiewicz, J., and Milosavljevic, A. (1992) Prototypic sequences, for human repetitive DNA.J. Mol. Evolution 35, 286–291.
Kyte, J. and Doolittle, R. F. (1982) A simple method for displaying the hydropathic character of a protein.J. Mol. Biol. 157, 105–132.
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.
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.
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.
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.
Staden, R. (1991) Screening protein and nucleic acid sequences against libraries of patterns.DNA Sequence 1, 369–374.
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.
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.
Gish, W. and States, D. J. (1993). Identification of protein coding regions by database similarity search.Nat. Genet. 3, 266–272.
Staden, R. (1989) Methods for calculating the probabilities of finding patterns in sequences.CABIOS 5, 89–96.
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.
Fickett, J. W. (1982) Recognition of protein coding regions in DNA sequences.Nucleic Acids Res. 10, 5303–5318.
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.
McLachlan, A.D. (1971) Test for comparing related amino acid sequences.J. Mol. Biol. 61, 409–424.
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.
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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