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Coincident indices of exons and introns

✍ Scribed by Jun Xu; Runsheng Chen; Lunjiang Ling; Ruoun Shen; Jian Sun

Book ID
103053389
Publisher
Elsevier Science
Year
1993
Tongue
English
Weight
708 KB
Volume
23
Category
Article
ISSN
0010-4825

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✦ Synopsis

In

this paper, the coincident index, proposed by W. F. Friedman in cryptology, is made use of in DNA sequence analysis and exon prediction. The coincident index of exons exceeds that of introns by many times, and is mainly affected by window length, which is correlated negatively with the coincident index. An optimal exon prediction scheme was obtained by experimental analysis with an orthogonal table. Besides exons, many other special sites such as tandem repeats can be identified by using the coincident index approach. The application of this approach to the ARV-2 (AIDS associated retrovirus 2) genome found three new possible coding regions and some unusual base composition regions which are probably related to definite biological functions.

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A method for concatenating exons from genomic DNA, thereby skipping large stretches of intron sequence, has been developed using the polymerase chain reaction (PCR) with primers based on known intronexon junction sequences. The use of genomic DNA circumvents the need for cDNA preparation for many pu