Chapter 3 An introduction to biological sequence analysis

New Comprehensive Biochemistry

Volumn 32, Issue C, 1998, Pages 29-42

  Fasman, KennethH ^a,b   Salzberg, StevenL ^a,b  

^a WHITEHEAD INSTITUTE FOR BIOMEDICAL RESEARCH   (United States)

^b Johns Hopkins University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 77956958680     PISSN: 01677306     EISSN: None     Source Type: Book Series    
DOI: 10.1016/S0167-7306(08)60460-3     Document Type: Chapter

References (55)

1. Gribskov M., and Devereux J. Sequence Analysis Primer (1991), Oxford University Press, Oxford
2. Doolittle R.F. In: Abelson J.N., and Simon M.I. (Eds). Computer Methods for Macromolecular Sequence Analysis, Vol. 266 of Methods in Enzymology (1996), Academic Press, San Diego, CA
3. Berg P., and Singer M. Dealing with Genes, The Language of Heredity (1992), University Science Books, Mill Valley, CA
4. Casey D. Primer on Molecular Genetics (1996), U.S. Department of Energy Human Genome Management Information System. http://www.ornl.gov/hgmis/publicat/primer/intro.html URL: http://www.ornl.gov/hgmis/publicat/primer/intro.html
5. Lewin B. Genes VI (1997), Oxford University Press, Oxford
6. Watson J.D., Gilman M., Witkowski J.A., and Zoller M.J. Recombinant DNA, 2nd edition (1992), Scientific American Books, New York
7. Staden R., and McLachlan A.D. Codon preference and its use in identifying protein coding regions in long DNA sequences. Nucleic Acids Res. 10 (1982) 141-156
8. Fickett J.W., and Tung C.S. Assessment of protein coding measures. Nucleic Acids Res. 20 (1992) 6441-6450
9. Krawczak M., and Cooper D.N. Single base-pair substitutions in pathology and evolution, two sides of the same coin. Hum. Mutation 8 (1996) 23-31
10. Kyte J., and Doolittle R.F. A simple method for displaying the hydropathic character of a protein. J. Mol. Biol. 157 (1982) 105-132
11. Matis S., Xu Y., Shah M., Guan X., Einstein J.R., Mural R., and Uberbacher E. Detection of RNA polymerase II promoters and polyadenylation sites in human DNA. Computer & Chemistry 20 (1996) 135-140
12. Smith T.F., and Waterman M.S. Comparison of biosequences. Adv. Appl. Math. 2 (1981) 482-489
13. Henikoff S., and Henikoff J.G. Amino acid substitution matrices from protein blocks. Proc. Natl. Acad. Sci. USA 89 (1992) 10915-10919
14. Dayhoff M.O. Atlas of Protein Sequence and Structure (1978), National Biomedical Research Foundation, Washington D.C
15. Altschul S.F. Amino acid substitution matrices from an information theoretic perspective. J. Mol. Biol. 219 (1991) 555-565
16. Gibbs A.J., and Mclntyre G.A. The diagram, a method for comparing sequences, its use with amino acid and nucleotide sequences. Eur. J. Biochem. 16 (1970) 1-11
17. Staden R. The Staden sequence analysis package. Mol. Biotechnol. 5 (1996) 233-241. http://www.mrc-lmb.cam.ac.uk/pubseq URL: http://www.mrc-lmb.cam.ac.uk/pubseq.
18. Benson D.A., Boguski M.S., Lipman D.J., and Ostell J. GenBank. Nucleic Acids Res. 25 (1997) 1-6
19. Stoesser G., Sterk P., Tuli M.A., Stoehr P.J., and Cameron G.N. The EMBL Nucleotide Sequence Database. Nucleic Acids Res. 25 (1997) 7-14
20. Bairoch A., and Apweiler R. The SWISS-PROT protein sequence data bank and its supplement TrEMBL. Nucleic Acids Res. 25 (1997) 31-36
21. Pearson W.R., and Lipman D.J. Improved tools for biological sequence comparison. Proc. Natl. Acad. Sci. USA 85 (1988) 2444-2448
22. Altschul S.F., Gish W., Miller W., Myers E.W., and Lipman D.J. Basic local alignment search tool. J. Mol. Biol 215 (1990) 403-410
23. Pearson W.R. Comparison of methods for searching protein sequence databases. Prot. Sci. 4 (1995) 1145-1160
24. Thompson J.D., Higgins D.G., and Gibson T.J. CLUSTALW, Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22 (1994) 4673-4680
25. Huang X. On global sequence alignment. Computer Applications in the Biosciences 10 (1994) 227-235
26. Lipman D.J., Altschul S.F., and Kececioglu J.D. A tool for multiple sequence alignment. Proc. Natl. Acad. Sci. USA 86 (1989) 4412-4415
27. Feng D.F., and Doolittle R.F. Progressive sequence alignment as a prerequisite to correct phylogenetic trees. J. Mol. Evol. 25 (1987) 351-360
28. Smith R.F., and Smith T.F. Pattern-Induced Multi-sequence Alignment (PIMA) algorithm employing secondary structure-dependent gap penalties for comparative protein modeling. Protein Eng. 5 (1992) 35-41
29. Henikoff S., Henikoff J.G., Afford W.J., and Pietrokovski S. Automated construction and graphical presentation of protein blocks from unaligned sequences. Gene 163 (1995) GC17-GC26
30. Schuler G.D., Altschul S.F., and Lipman D.J. A workbench for multiple alignment construction and analysis. Proteins Struct. Funct. Genet. 9 (1991) 180-190
31. Grundy W., Bailey T., Elkan C., and Baker M. Meta-MEME, motif-based hidden Markov models of protein families. Computer Applications in the Biosciences 13 (1997) 397-403
32. Krogh A., Brown M., Mian I.S., Sjolander K., and Haussler D. Hidden Markov models in computational biology, applications to protein modeling. J. Mol. Biol. 235 (1994) 1501-1531
33. Myers E., Selznick S., Zhang Z., and Miller W. Progressive multiple alignment with constraints. J. Comput. Biol. 3 (1996) 563-572
34. Felsenstein J. PHYLIP - Phylogeny Inference Package (Version 3.2). Cladistics 5 (1989) 164-166. http://evolution.genetics.washington.edu/phylip.html URL: http://evolution.genetics.washington.edu/phylip.html.
35. Swofford D.L. PAUP, Phylogenetic Analysis Using Parsimony, Users Manual, Version 3.5 (1990), Illinois Natural History Survey, Champaign, IL
36. Daly, M.J. and Lander, E.S. Alewife sequence assembler. Manuscript in preparation
37. Larson S., Jain M., Anson E., and Myers E. An interface for a fragment assembly kernel. Tech. Rep. TR96-04 (1996), Dept. of Computer Science, University of Arizona, Tucson, AZ
38. Huang X. An improved sequence assembly program. Genomics 33 (1996) 21-31
39. Bonfield J.K., Smith K.F., and Staden R. A new DNA sequence assembly program. Nucleic Acids Res. 24 (1995) 4992-4999
40. Fleischmann R.D., Adams M., White O., Clayton R., Kirkness E., Kerlavage A., Bult C., Tomb J.F., Dougherty B., Merrick J., McKenney K., Sutton G., FitzHugh W., Fields C., Gocayne J., Scott J., Shirley R., Liu L.I., Glodek A., Kelley J., Weidman J., Phillips C., Spriggs T., Hedblom E., Cotton M., Utterback T., Hanna M., Nguyen D., Saudek D., Brandon R., Fine L., Fritchman J., Fuhrmann J., Geoghagen N., Gnehm C., McDonald L., Small K., Fraser C., Smith H.O., and Venter J.C. Whole-genome random sequencing, assembly of Haemophilus influenzae Rd. Science 269 (1995) 496-512
41. Fraser C., Gocayne J., White O., Adams M., Clayton R., Fleischmann R., Bult C., Kerlavage A., Sutton G., Kelley J., Fritchman J., Weidman J., Small K., Sandusky M., Fuhrmann J., Nguyen D., Utterback T., Saudek R., Phillips C., Merrick J., Tomb J.F., Dougherty B., Bott K., Hu P.C., Lucier T., Peterson S., Smith H.O., Hutchison C., and Venter J.C. The minimal gene complement of Mycoplasma genitalium. Science 270 (1995) 397-403
42. Sutton G., White O., Adams M., and Kerlavage A. TIGR Assembler, a new tool for assembling large shotgun sequencing projects. Genome Science Tech. 1 (1995) 9-19
43. Wootton J.C., and Federhen S. Statistics of local complexity in amino acid sequences and sequence databases. Comput. & Chem. 17 (1993) 149-163
44. Claverie J.M., and States D. Information enhancement methods for large scale sequence analysis. Comput. & Chem. 17 (1993) 191-201
45. Jurka J., Klonowski P., Dagman V., and Pelton P. CENSOR - a program for identification and elimination of repetitive elements from DNA sequences. Comput. & Chem. 20 (1996) 119-122
46. Smit, A.F.A. and Green, P. (1996) RepeatMasker. URL: http://ftp.genome.washington.edu/RM/RepeatMasker.html
47. Adams M.D., Kelley J.M., Gocayne J.D., Dubnick M., Polymeropoulos M.H., Xiao H., Merril C.R., Wu A., Olde B., Moreno R.F., et al. Complementary DNA sequencing: expressed sequence tags and human genome project. Science 252 (1991) 1651-1656
48. Adams M.D., Kerlavage A.R., Fleischmann R.D., et al. Initial assessment of human gene diversity and expression patterns based upon 83 million nucleotides of cDNA sequence. Nature 377 Suppl. (1995) 3-174
49. Boguski M.S., and Schuler G.D. ESTablishing a human transcript map. Nat. Genet. 10 (1995) 369-371
50. Aaronson J.S., Eckman B., Blevins R.A., Borkowski J.A., Myerson J., Imran S., and Elliston K.O. Toward the development of a gene index to the human genome: an assessment of the nature of high-throughput EST sequence data. Genome Res. 6 (1996) 829-845
51. Fickett J.W. Recognition of protein coding regions in DNA sequences. Nucleic Acids Res. 10 (1982) 5303-5318
52. Borodovsky M., and Mcininch J.D. GeneMark, parallel gene recognition for both DNA strands. Comput. & Chem. 17 (1993) 123-133
53. Salzberg S., Delcher A., Kasif S., and White O. Microbial gene identification using interpolated Markov models. Nucleic Acids Res. 26 (1998) 544-548
54. White O., Dunning T., Sutton G., Adams M., Venter J.C., and Fields C. A quality control algorithm for DNA sequencing projects. Nucleic Acids Res. 21 (1993) 3829-3838
55. Hannenhalli S., Chappey C., Koonin E.V., and Pevzner P.A. Genome sequence comparison and scenarios for gene rearrangements, a test case. Genomics 30 (1995) 299-311