The staden sequence analysis package

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/.

[1]  R Staden,et al.  An interactive graphics program for comparing and aligning nucleic acid and amino acid sequences. , 1982, Nucleic acids research.

[2]  J. Bonfield,et al.  A new DNA sequence assembly program. , 1995, Nucleic acids research.

[3]  J. Garnier,et al.  Analysis of the accuracy and implications of simple methods for predicting the secondary structure of globular proteins. , 1978, Journal of molecular biology.

[4]  W R Pearson,et al.  Using the FASTA program to search protein and DNA sequence databases. , 1994, Methods in molecular biology.

[5]  R. Staden.  Finding protein coding regions in genomic sequences. , 1990, Methods in enzymology.

[6]  John K. Ousterhout,et al.  Tcl and the Tk Toolkit , 1994 .

[7]  Rodger Staden,et al.  Methods to define and locate patterns of motifs in sequences , 1988, Comput. Appl. Biosci..

[8]  R. Staden.  Searching for patterns in protein and nucleic acid sequences. , 1990, Methods in enzymology.

[9]  R Staden.  Computer methods to locate signals in nucleic acid sequences , 1984, Nucleic Acids Res..

[10]  D. Eisenberg,et al.  Analysis of membrane and surface protein sequences with the hydrophobic moment plot. , 1984, Journal of molecular biology.

[11]  David J. States,et al.  Identification of protein coding regions by database similarity search , 1993, Nature Genetics.

[12]  R Staden,et al.  Indexing the sequence libraries: software providing a common indexing system for all the standard sequence libraries. , 1992, DNA sequence : the journal of DNA sequencing and mapping.

[13]  R. Staden.  Sequence data handling by computer. , 1977, Nucleic acids research.

[14]  Rodger Staden,et al.  Methods for calculating the probabilities of finding patterns in sequences , 1989, Comput. Appl. Biosci..

[15]  J. Fickett.  Recognition of protein coding regions in DNA sequences. , 1982, Nucleic acids research.

[16]  R. Staden,et al.  A standard file format for data from DNA sequencing instruments. , 1992, DNA sequence : the journal of DNA sequencing and mapping.

[17]  R. Staden.  Automation of the computer handling of gel reading data produced by the shotgun method of DNA sequencing. , 1982, Nucleic acids research.

[18]  R Staden,et al.  Screening protein and nucleic acid sequences against libraries of patterns. , 1991, DNA sequence : the journal of DNA sequencing and mapping.

[19]  R Staden,et al.  A computer program to search for tRNA genes. , 1980, Nucleic acids research.

[20]  J. Bonfield,et al.  Experiment files and their application during large-scale sequencing projects. , 1996, DNA sequence : the journal of DNA sequencing and mapping.

[21]  R. Doolittle,et al.  A simple method for displaying the hydropathic character of a protein. , 1982, Journal of molecular biology.

[22]  Rodger Staden,et al.  A computer program to enter DNA gel reading data into a computer , 1984, Nucleic Acids Res..

[23]  Rodger Staden,et al.  Computer Methods to Locate Genes and Signals in Nucleic Acid Sequences , 1985 .

[24]  A. D. McLachlan,et al.  Codon preference and its use in identifying protein coding regions in long DNA sequences , 1982, Nucleic Acids Res..

[25]  Rodger Staden,et al.  Measurements of the effects that coding for a protein has on a DNA sequence and their use for finding genes , 1984, Nucleic Acids Res..

[26]  R Staden,et al.  The application of numerical estimates of base calling accuracy to DNA sequencing projects. , 1995, Nucleic acids research.

[27]  M. Schiffer,et al.  Use of helical wheels to represent the structures of proteins and to identify segments with helical potential. , 1967, Biophysical journal.

[28]  A. Mclachlan.  Tests for comparing related amino-acid sequences. Cytochrome c and cytochrome c 551 . , 1971, Journal of molecular biology.

[29]  Rodger Staden,et al.  Methods for discovering novel motifs in nucleic acid sequences , 1989, Comput. Appl. Biosci..

[30]  R. Staden.  A new computer method for the storage and manipulation of DNA gel reading data. , 1980, Nucleic acids research.