A strategy for finding regions of similarity in complete genome sequences

MOTIVATION: Complete genomic sequences will become available in the future. New methods to deal with very large sequences (sizes beyond 100 kb) efficiently are required. One of the main aims of such work is to increase our understanding of genome organization and evolution. This requires studies of the locations of regions of similarity. RESULTS: We present here a new tool, ASSIRC ('Accelerated Search for SImilarity Regions in Chromosomes'), for finding regions of similarity in genomic sequences. The method involves three steps: (i) identification of short exact chains of fixed size, called 'seeds', common to both sequences, using hashing functions; (ii) extension of these seeds into putative regions of similarity by a 'random walk' procedure; (iii) final selection of regions of similarity by assessing alignments of the putative sequences. We used simulations to estimate the proportion of regions of similarity not detected for particular region sizes, base identity proportions and seed sizes. This approach can be tailored to the user's specifications. We looked for regions of similarity between two yeast chromosomes (V and IX). The efficiency of the approach was compared to those of conventional programs BLAST and FASTA, by assessing CPU time required and the regions of similarity found for the same data set. AVAILABILITY: Source programs are freely available at the following address: ftp://ftp.biologie.ens. fr/pub/molbio/assirc.tar.gz CONTACT: vincens@biologie.ens.fr, hazout@urbb.jussieu.fr      

Radioimmunoassay of plasma 21-deoxycortisol

A reliable radioimmunoassay for the determination of plasma 21-deoxycortisol (21-DF) after chromatography on Sephadex LH20 columns of methylene chloride plasma extracts has been described and evaluated. The antiserum used was raised in rabbits injected with 21-DF-3-(O-carboxy-methyl)oxime-bovine serum albumin. In men (n = 10) the levels ranged from 0.11 to 0.29 ng/ml (mean +/- SD: 0.21 +/- 0.06). In women the mean levels were in the follicular phase: 0.16 +/- 0.06 (range: 0.05-0.22; n = 10) and in the luteal phase: 0.18 +/- 0.06 (range: 0.10-0.35; n = 12). No cyclical change and no significant difference between male and female groups were observed. In patients with congenital adrenal hyperplasia due to 21-hydroxylase deficiency very high levels were observed. The higher concentration of 21-DF found in adrenal effluent than in peripheral plasma has provided direct evidence of its adrenal origin in patients without 21-hydroxylase deficiency.