Daniel P. Berrar, Werner Dubitzky, Martin Granzow's A Practical Approach to Microarray Data Analysis PDF

By Daniel P. Berrar, Werner Dubitzky, Martin Granzow

ISBN-10: 1402072600

ISBN-13: 9781402072604

The e-book addresses the requirement of scientists and researchers to achieve a simple knowing of microarray research methodologies and instruments. it really is meant for college kids, lecturers, researchers, and learn managers who are looking to comprehend the cutting-edge and of the provided methodologies and the components during which gaps in our wisdom call for additional learn and improvement. The publication is designed for use by way of the working towards specialist tasked with the layout and research of microarray experiments or as a textual content for a senior undergraduate- or graduate point path in analytical genetics, biology, bioinformatics, computational biology, records and information mining, or utilized laptop technology.

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REFERENCES 27 32. Gusfield D. Efficient methods for multiple sequence alignment with guaranteed error bounds. Bull Math Biol 1993;55:141. 33. Henikoff S, Henikoff JG. Amino acid substitution matrices from protein blocks. Proc Natl Acad Sci USA 1992;89:10915. 34. Herschlag D. RNA chaperones and the RNA folding problem. J Biol Chem 1995;270:20781. 35. Hirschberg DS. A linear space algorithm for computing maximal common subsequences. Commun ACM 1975;18:341. 36. Hofacker IL, Fekete M, Stadler PF. Secondary structure prediction for aligned RNA sequences.

2 Alignment of RNA Sequences with Known Secondary Structures Since the secondary structures are preserved among RNA sequences with similar function, it is important to incorporate them when comparing RNA sequences. , structure unknown) [41]. As result, there are six different 22 DYNAMIC PROGRAMMING ALGORITHMS computational problems that can be formulated for a pairwise comparison of RNA sequences: Align(crossing, crossing), for aligning two RNA sequences both with pseudoknotted structures; Align(crossing, nested), for aligning one RNA sequence with pseudoknotted structures and another RNA sequence without pseudoknotted structure; Align(crossing, plain), for aligning one RNA sequence with pseudoknotted structures and another RNA sequence without known structure; Align(nested, nested), for aligning two RNA sequences both without pseudoknotted structures; Align(nested, plain), for aligning one RNA sequence with known nonpseudoknotted structures and another RNA sequence without known structure; Align(plain, plain), for aligning two RNA sequences without known structures.

Dayhoff MA, Schwartz RM, Orcutt BC. A model of evolutionary change in proteins. Atlas of Protein Sequence and Structure. Chapter 5, 1978. p345. 22. Delcher AL, Kasif S, Fleischman RD, Peterson J, White O, Salzberg SL. Alignment of whole genomes. Nucleic Acid Res 1999;27(11):2369–2376. 23. Do CB, Brudno M, Batzoglou S. ProbCons: probabilistic consistencybased multiple alignment of amino acid sequences. Genome Res 2005;15:330. 24. Dost B, Han B, Zhang S, Bafna V. Structural alignment of pseudoknotted RNA.

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A Practical Approach to Microarray Data Analysis by Daniel P. Berrar, Werner Dubitzky, Martin Granzow

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