Gene identification approaches

Search for nonrandom similarity with consensus sequences 

A statistical method for estimating the significance of the similarity between a consensus of a functional signal and a similar sequence fragment is briefly described below [22, 23]. 

Let us assume that we are searching for a site in a sequence of length N with a random arrangement of nucleotides A, T(U), G and C, where the frequencies of these nucleotides are PA, Pt u), Pc and Pc, respectively. If we accept that Pi = PA, P2 = Pg, P3 = Pt, Pa = Pc, then the frequencies of the nucleotides of the other classes Pj (j = 5. 15) representing the nonempty subsets of the set A, C, G, T of nucleotides are determined as sums of frequencies of nucleotides of all the types of the j-th class. Pi5 represents the set of all 4 nucleotides, depicted by the IUPAC code N. 

In this case the expected number T(L,k) of structures (L,k) in a random sequence of length N is  

Here PL is the number of possible site positions in the sequence Fl = N-L+ 1. 

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SEQUENCE-BASED APPROACHES TO ALKALOID BIOSYNTHESIS GENE IDENTIFICATION... 

This chapter is an historical perspective with selected examples from our own laboratory, first at the University of Munich, and now at the Leibniz Institute of Plant Biochemistry in Halle, that reflect the changes in how we define and exploit sequence-based approaches to alkaloid biosynthesis gene identification. ... 

Sequence-Based Approaches to Alkaloid Biosynthesis Gene Identification... 163 Toni M. Kutchan... 

Reliable criteria to identify the (individual) patients suitable for high-LET radiation therapy need to be developed. At present, the available criteria are derived (mainly) from the clinical fast neutron experience. It can be expected that novel approaches based on modern techniques involving molecular biology or gene identification may provide appropriate and still missing information. They may also provide information on the susceptibility or risk for secondary radio-induced cancer. 

Wayne, M. L., and McIntyre, L. M., 2002, Combining mapping and arraying an approach to candidate gene identification, Proc. Natl. Acad. Sci. USA 99 14903-14906. 

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