The comparison of protein and DNA sequences is an important analytical method of applied bioinformatics. The annotations of new nucleotide and protein sequences, construction of model structures for proteins, design and analysis of expression studies as well as a variety of other bioinformatic and biological experiments are all based on these analyses. Nature acts conservatively, i.e., it does not develop a new kind of biology for every life form but continuously changes and adapts a proven general concept. Novel functionalities do not appear because a new gene has suddenly arisen but are developed and modi- fi ed during evolution. Given this situation, therefore, one may transfer functional information from one protein to another if both possess a certain degree of similarity. However, this process must be carried out critically, as similar proteins may yet perform different functions, despite, for example, having arisen from a common ancestor.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410
Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389–3402
Dayhoff MO, Schwartz RM, Orcutt BC (1978) In: Dayhoff MO (ed) Atlas of protein sequence and structure, vol. 5, suppl. 3, p 345, NBRF, Washington/DC
Eddy SR (2004) What is a hidden Markov model? Nat Biotechnol 10:1315–1316
Gerlt J, Babbitt P (2001) Respond: Orthologs and paralogs – we need to get it right. Genome Biol 2(8):1002.1–1002.3
Henikoff SB, Henikoff JG (1992) Amino acid substitution matrices from protein blocks. Proc Natl Acad Sci USA 89:10915–10919
Jensen RA (2001) Correspondence: Orthologs and paralogs – we need to get it right. Genome Biol 2(8):1002.1–1002.3
Ma B, Tromp J, Li M (2002) PatternHunter: faster and more sensitive homology search. Bioinformatics 18:440–445
Needleman SB, Wunsch CD (1970) A general method applicable to the search for similarities in the amino acid sequence of two proteins. J Mol Biol 48:443–453
Pearson WR, Lipman DJ (1998) Improved tools for biological sequence comparison. Proc Natl Acad Sci USA 4:2444–2448
Rice P, Longden I, Bleasby A (2000) EMBOSS: the European molecular biology open software suite. Trends Genet 16:276–277
Smith TF, Waterman MS (1981) Identification of common molecular subsequences. J Mol Biol 147:195–197
Tatusov RL, Koonin EV, Lipman DJ (1997) A genomic perspective on protein families. Science 287:631–637
Tatusova TA, Madden TL (1999) Blast 2 sequences – a new tool for comparing protein and nucleotide sequences. FEMS Microbiol Lett 174:247–250
Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673–4680
Zhang Z, Schaffer AA, Miller W, Madden TL, Lipman DJ, Koonin EV, Altschul SF (1998) Protein sequence similarity searches using patterns as seeds. Nucleic Acids Res 26:3986–3990
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2008 Springer-Verlag Berlin Heidelberg
About this chapter
Cite this chapter
(2008). Sequence Comparisons and Sequence-Based Database Searches. In: Selzer, P.M., Marhöfer, R.J., Rohwer, A. (eds) Applied Bioinformatics. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-72800-9_4
Download citation
DOI: https://doi.org/10.1007/978-3-540-72800-9_4
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-72799-6
Online ISBN: 978-3-540-72800-9
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)