academic/staden: Added (DNA sequence assembly, editing, and analysis tools)

Signed-off-by: Robby Workman <rworkman@slackbuilds.org>

1 files changed, 117 insertions, 0 deletions

diff --git a/academic/staden/References b/academic/staden/References
new file mode 100644
index 0000000000..a08f2a4763
--- /dev/null
+++ b/academic/staden/References
@@ -0,0 +1,117 @@
+Recent publications from the group include:
+
+    Bonfield, James K. and Whitwham, Andrew. Gap5 - editing the billion fragment sequence assembly. Bioinformatics 26, 1699-1703, (2010)
+
+    Rodger Staden, David P. Judge and James K. Bonfield. Managing Sequencing Projects in the GAP4 Environment. Introduction to Bioinformatics. A Theoretical and Practical Approach. Eds. Stephen A. Krawetz and David D. Womble. Human Press Inc., Totawa, NJ 07512 (2003)
+
+    Rodger Staden, David P. Judge and James K. Bonfield. Analysing Sequences Using the Staden Package and EMBOSS. Introduction to Bioinformatics. A Theoretical and Practical Approach. Eds. Stephen A. Krawetz and David D. Womble. Human Press Inc., Totawa, NJ 07512 (2003)
+
+    Bonfield, James K. and Staden, Rodger. ZTR: a new format for DNA sequence trace data. Bioinformatics 18, 3-10, (2002).
+
+    Bonfield, James, K., Beal, Kathryn F., Betts, Matthew J. and Staden, Rodger. Trev: a DNA trace editor and viewer. Bioinformatics 18, 194-195, (2002)
+
+    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.
+
+    The C. elegans Sequencing Consortium. Genome Sequence of the Nematode C. elegans: A Platform for Investigating Biology. Science 282, 2012-2018 (1998)
+
+    Rodger Staden, Kathryn F. Beal and James K. Bonfield The Staden Package, 1998. Computer Methods in Molecular Biology, pages 115-130, vol. 132: Bioinformatics Methods and Protocols Eds Stephen Misener and Steve A. Krawetz. The Humana Press Inc., Totowa, NJ 07512
+
+    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)
+
+    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)
+
+    Staden, R. The Staden Sequence Analysis Package. Molecular Biotechnology 5, 233-241 (1996)
+
+    Bonfield, J.K. and Staden, R. Experiment files and their application during large-scale sequencing projects. DNA Sequence 6, 109-117 (1996)
+
+    Staden, R. Indexing and using sequence databases. Methods in Enzymology 266, 105-114 (1996)
+
+    Bonfield, J.K., Smith, K.F. and Staden, R. A new DNA sequence assembly program. Nucleic Acids Res. 23, 4992-4999 (1995)
+
+    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)
+
+    Dear, S. and Staden, R. A standard file format for data from DNA sequencing instruments. DNA Sequence 3, 107-110 (1992)
+
+    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).
+
+    Dear, S. and Staden, R. A sequence assembly and editing program for efficient management of large projects. Nucleic Acid Res. 19, 3907-3911 (1991).
+
+    Staden, R. Screening protein and nucleic acid sequences against libraries of patterns. DNA Sequence 1, 369-374 (1991).
+
+    Gleeson TJ, Staden R. An X windows and UNIX implementation of our sequence analysis package. Comput Applic Biosci. 7, 398 (1991)
+
+    Gleeson, T. and Hillier, L. A trace display and editing program for data from fluorescence based sequencing machines Nuc. Acids Res. 19, 6481-6483 (1991)
+
+    Staden, R. Searching for patterns in protein and nucleic acid sequences. Methods in Enzymology 183, 193-211. (1990).
+
+    Staden, R. Finding protein coding regions in genomic sequences. Methods in Enzymology 183, 163-180. (1990).
+
+Older publications relating to the package include:
+
+    Staden, R. Methods for discovering novel motifs in nucleic acid sequences. Comput Applic Biosc 5, 293-298 (1989)
+
+    Staden R, Methods for calculating the probabilities of finding patterns in sequences. Comput Applic Biosci 5 89-96 (1989)
+
+    Staden R, Methods to define and locate patterns of motifs in sequences. Comput Applic Biosci 4, 53-60 (1988)
+
+    Staden, R. Computer methods to locate genes and signals in nucleic acid sequences. In Genetic Engineering Principles and Methods, vol 7, pages 67-114, Eds Setlow, J.K. and Hollaender, A, Plenum, NY, USA (1985).
+
+    McLachlan AD, Staden R, Boswell DR. A method for measuring the non-random bias of a codon usage table. Nucleic Acids Res. 12, 9567-75. (1984)
+
+    Staden, R. Graphic methods to determine the function of nucleic acid sequences. Nucleic Acid Res. 12, 521-538 (1984)
+
+    Staden, R. Computer methods to locate signals in nucleic acid sequences. Nucleic Acid Res. 12, 505-519 (1984)
+
+    Staden, R. A computer program to enter DNA gel reading data into a computer. Nucleic Acid Res. 12, 499-503 (1984)
+
+    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)
+
+    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)
+
+    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)
+
+    Staden, R. An interactive graphics program for comparing and aligning nucleic acid and amino acid sequences. Nucleic Acid Res. 10, 2951-2961 (1982)
+
+    Staden, R. A new computer method for the storage and manipulation of DNA gel reading data. Nucleic Acid Res. 8, 3673-3694 (1980)
+
+    Staden, R. A computer program to search for tRNA genes. Nucleic Acid Res. 8, 817-825 (1980)
+
+    Staden R. A strategy of DNA sequencing employing computer programs. Nucleic Acids Res. 6, 2601-10 (1979)
+
+    Staden R. Further procedures for sequence analysis by computer Nucleic Acids Res. 5, 1013-1016 (1978)
+
+    Staden R. Sequence data handling by computer Nucleic Acids Res. 4, 4037-4051 (1977)
+
+Other papers by Rodger Staden
+
+    Cesar Milstein, Michael S. Neuberger and Rodger Staden. Both DNA strands of antibody genes are hypermutation targets. Proc. Natl. Acad. Sci. USA, 95, 8791-8794 (1998)
+
+    Perutz MF, Staden R, Moens L and De Baere I. Polar Zippers Current Biology 3, 249-253 (1993)
+
+    Sulston J, Du Z, Thomas K, Wilson R, Hillier L, Staden R, Halloran N, Green P, Thierry-Mieg J, Qiu L, et al. The C. elegans genome sequencing project: a beginning Nature 356, 37-41 (1992)
+
+    Honess RW, Gompels UA, Barrell BG, Craxton M, Cameron KR, Staden R, Chang YN, Hayward GS. Deviations from expected frequencies of CpG dinucleotides in herpesvirus DNAs may be diagnostic of differences in the states of their latent genomes J Gen Virol. 70 (Pt 4) 837-55 (1989)
+
+    Sulston J, Mallett F, Staden R, Durbin R, Horsnell T, Coulson A. Software for genome mapping by fingerprinting techniques. Comput Applic Biosci. 4 125-32 (1988)
+
+    Anderson S, Bankier AT, Barrell BG, de Bruijn MH, Coulson AR, Drouin J, Eperon IC, Nierlich DP, Roe BA, Sanger F, Schreier PH, Smith AJ, Staden R, Young IG. Comparison of the Human and Bovine Mitochondrial Genomes Mitochondrial Genes, 5-43, Cold Spring Harbor Laboratory, USA (1982)
+
+    Woo SL, Beattie WG, Catterall JF, Dugaiczyk A, Staden R, Brownlee GG, O'Malley BW. Complete nucleotide sequence of the chicken chromosomal ovalbumin gene and its biological significance Biochemistry 20, 6437-46 (1981)
+
+    Griffin BE, Soeda E, Barrell BG, Staden R. Sequences and analysis of polyoma virus DNA. In Tooze J (ed) DNA tumor viruses, 2nd edn. Cold Spring Harbor Laboratory, New York, pp 843-910 (1981)
+
+    Anderson S, Bankier AT, Barrell BG, de Bruijn MH, Coulson AR, Drouin J, Eperon IC, Nierlich DP, Roe BA, Sanger F, Schreier PH, Smith AJ, Staden R, Young IG. Sequence and organization of the human mitochondrial genome Nature. 290, 457-65 (1981)
+
+    Barrell BG, Anderson S, Bankier AT, de Bruijn MH, Chen E, Coulson AR, Drouin J, Eperon IC, Nierlich DP, Roe BA, Sanger F, Schreier PH, Smith AJ, Staden R, Young IG. Sequence of Mammalian Mitochondrial DNA Colloquium der Gesellscaft fur Biologische Chemie, 14-19 April 1980 in Mosbach/Baden, 11-25, (1980).
+
+    Barrell BG, Anderson S, Bankier AT, de Bruijn MH, Chen E, Coulson AR, Drouin J, Eperon IC, Nierlich DP, Roe BA, Sanger F, Schreier PH, Smith AJ, Staden R, Young IG. Different pattern of codon recognition by mammalian mitochondrial tRNAs Proc Natl Acad Sci U S A. 77 3164-6 (1980)
+
+    Robertson MA, Staden R, Tanaka Y, Catterall JF, O'Malley BW, Brownlee GG. Sequence of three introns in the chick ovalbumin gene Nature 278, 370-372 (1979)
+
+    Godson GN, Barrell BG, Staden R, Fiddes JC. Nucleotide sequence of bacteriophage G4 DNA Nature 276, 236-247 (1978)
+
+    Catterall JF, O'Malley BW, Robertson MA, Staden R, Tanaka Y, Brownlee GG. Nucleotide sequence homology at 12 intron--exon junctions in the chick ovalbumin gene Nature 275, 510-513 (1978)
+
+    Bloomer AC, Champness JN, Bricogne G, Staden R and Klug A Protein disk of tobacco mosaic virus at 2.8A resolution showing the interactions within and between subunits Nature 276, 362-368 (1978) 
+
+Observation test: did you spot the co-authors who, so far, have won 6 Nobel prizes?