José L. Oliver

The general stochastic model of nucleotide substitution

DNA sequence evolution through nucleotide substitution may be assimilated to a stationary Markov process. The fundamental equations of the general model, with 12 independent substitution parameters, are used to obtain a formula which corrects the effect of multiple and parallel substitutions on the measure of evolutionary divergence between two homologous sequences. We show that only reversible models, with six independent parameters, allow the calculation of the substitution rates. Simulation experiments on DNA sequence evolution through nucleotide substitution call into question the effectiveness of the general model (and of any other more detailed description); nevertheless, the general model results are slightly superior to any of its particular cases.

CpGcluster: a distance-based algorithm for CpG-island detection

BackgroundDespite their involvement in the regulation of gene expression and their importance as genomic markers for promoter prediction, no objective standard exists for defining CpG islands (CGIs), since all current approaches rely on a large parameter space formed by the thresholds of length, CpG fraction and G+C content.ResultsGiven the higher frequency of CpG dinucleotides at CGIs, as compared to bulk DNA, the distance distributions between neighboring CpGs should differ for bulk and island CpGs. A new algorithm (CpGcluster) is presented, based on the physical distance between neighboring CpGs on the chromosome and able to predict directly clusters of CpGs, while not depending on the subjective criteria mentioned above. By assigning a p-value to each of these clusters, the most statistically significant ones can be predicted as CGIs. CpGcluster was benchmarked against five other CGI finders by using a test sequence set assembled from an experimental CGI library. CpGcluster reached the highest overall accuracy values, while showing the lowest rate of false-positive predictions. Since a minimum-length threshold is not required, CpGcluster can find short but fully functional CGIs usually missed by other algorithms. The CGIs predicted by CpGcluster present the lowest degree of overlap with Alu retrotransposons and, simultaneously, the highest overlap with vertebrate Phylogenetic Conserved Elements (PhastCons). CpGclusters CGIs overlapping with the Transcription Start Site (TSS) show the highest statistical significance, as compared to the islands in other genome locations, thus qualifying CpGcluster as a valuable tool in discriminating functional CGIs from the remaining islands in the bulk genome.ConclusionCpGcluster uses only integer arithmetic, thus being a fast and computationally efficient algorithm able to predict statistically significant clusters of CpG dinucleotides. Another outstanding feature is that all predicted CGIs start and end with a CpG dinucleotide, which should be appropriate for a genomic feature whose functionality is based precisely on CpG dinucleotides. The only search parameter in CpGcluster is the distance between two consecutive CpGs, in contrast to previous algorithms. Therefore, none of the main statistical properties of CpG islands (neither G+C content, CpG fraction nor length threshold) are needed as search parameters, which may lead to the high specificity and low overlap with spurious Alu elements observed for CpGcluster predictions.

Genetic relationships among melon breeding lines revealed by RAPD markers and agronomic traits

Abstract RAPD markers and agronomic traits were used to determine the genetic relationships among 32 breeding lines of melon belonging to seven varietal types. Most of the breeding lines were Galia and Piel de Sapo genotypes, which are currently being used in breeding programmes to develop new hybrid combinations. A total of 115 polymorphic reliable bands from 43 primers and 24 agronomic traits were scored for genetic distance calculations and cluster analysis. A high concordance between RAPDs and agronomic traits was observed when genetic relationships among lines were assessed. In addition, RAPD data were highly correlated with the pedigree information already known for the lines and revealed the existence of two clusters for each varietal type that comprised the lines sharing similar agronomic features. These groupings were consistent with the development of breeding programmes trying to generate two separate sets of parental lines for hybrid production. Nevertheless, the performance of certain hybrids indicated that RAPDs were more suitable markers than agronomic traits in predicting genetic distance among the breeding lines analysed. The employment of RAPDs as molecular markers both in germplasm management and improvement, as well as in the selection of parental lines for the development of new hybrid combinations, is discussed.

A Relationship Between GC Content and Coding-Sequence Length

Since base composition of translational stop codons (TAG, TAA, and TGA) is biased toward a low G+C content, a differential density for these termination signals is expected in random DNA sequences of different base compositions. The expected length of reading frames (DNA segments of sense codons flanked by in-phase stop codons) in random sequences is thus a function of GC content. The analysis of DNA sequences from several genome databases stratified according to GC content reveals that the longest coding sequences—exons in vertebrates and genes in prokaryotes—are GC-rich, while the shortest ones are GC-poor. Exon lengthening in GC-rich vertebrate regions does not result, however, in longer vertebrate proteins, perhaps because of the lower number of exons in the genes located in these regions. The effects on coding-sequence lengths constitute a new evolutionary meaning for compositional variations in DNA GC content.

Isochore chromosome maps of eukaryotic genomes

Analytical DNA ultracentrifugation revealed that eukaryotic genomes are mosaics of isochores: long DNA segments (>>300 kb on average) relatively homogeneous in G+C. Important genome features are dependent on this isochore structure, e.g. genes are found predominantly in the GC-richest isochore classes. However, no reliable method is available to rigorously partition the genome sequence into relatively homogeneous regions of different composition, thereby revealing the isochore structure of chromosomes at the sequence level. Homogeneous regions are currently ascertained by plain statistics on moving windows of arbitrary length, or simply by eye on G+C plots. On the contrary, the entropic segmentation method is able to divide a DNA sequence into relatively homogeneous, statistically significant domains. An early version of this algorithm only produced domains having an average length far below the typical isochore size. Here we show that an improved segmentation method, specifically intended to determine the most statistically significant partition of the sequence at each scale, is able to identify the boundaries between long homogeneous genome regions displaying the typical features of isochores. The algorithm precisely locates classes II and III of the human major histocompatibility complex region, two well-characterized isochores at the sequence level, the boundary between them being the first isochore boundary experimentally characterized at the sequence level. The analysis is then extended to a collection of human large contigs. The relatively homogeneous regions we find show many of the features (G+C range, relative proportion of isochore classes, size distribution, and relationship with gene density) of the isochores identified through DNA centrifugation. Isochore chromosome maps, with many potential applications in genomics, are then drawn for all the completely sequenced eukaryotic genomes available.

sRNAtoolbox: an integrated collection of small RNA research tools

Small RNA research is a rapidly growing field. Apart from microRNAs, which are important regulators of gene expression, other types of functional small RNA molecules have been reported in animals and plants. MicroRNAs are important in host-microbe interactions and parasite microRNAs might modulate the innate immunity of the host. Furthermore, small RNAs can be detected in bodily fluids making them attractive non-invasive biomarker candidates. Given the general broad interest in small RNAs, and in particular microRNAs, a large number of bioinformatics aided analysis types are needed by the scientific community. To facilitate integrated sRNA research, we developed sRNAtoolbox, a set of independent but interconnected tools for expression profiling from high-throughput sequencing data, consensus differential expression, target gene prediction, visual exploration in a genome context as a function of read length, gene list analysis and blast search of unmapped reads. All tools can be used independently or for the exploration and downstream analysis of sRNAbench results. Workflows like the prediction of consensus target genes of parasite microRNAs in the host followed by the detection of enriched pathways can be easily established. The web-interface interconnecting all these tools is available at http://bioinfo5.ugr.es/srnatoolbox

IsoFinder: computational prediction of isochores in genome sequences

Isochores are long genome segments homogeneous in G+C. Here, we describe an algorithm (IsoFinder) running on the web (http://bioinfo2.ugr.es/IsoF/isofinder.html) able to predict isochores at the sequence level. We move a sliding pointer from left to right along the DNA sequence. At each position of the pointer, we compute the mean G+C values to the left and to the right of the pointer. We then determine the position of the pointer for which the difference between left and right mean values (as measured by the t-statistic) reaches its maximum. Next, we determine the statistical significance of this potential cutting point, after filtering out short-scale heterogeneities below 3 kb by applying a coarse-graining technique. Finally, the program checks whether this significance exceeds a probability threshold. If so, the sequence is cut at this point into two subsequences; otherwise, the sequence remains undivided. The procedure continues recursively for each of the two resulting subsequences created by each cut. This leads to the decomposition of a chromosome sequence into long homogeneous genome regions (LHGRs) with well-defined mean G+C contents, each significantly different from the G+C contents of the adjacent LHGRs. Most LHGRs can be identified with Bernardis isochores, given their correlation with biological features such as gene density, SINE and LINE (short, long interspersed repetitive elements) densities, recombination rate or single nucleotide polymorphism variability. The resulting isochore maps are available at our web site (http://bioinfo2.ugr.es/isochores/), and also at the UCSC Genome Browser (http://genome.cse.ucsc.edu/).

APPLICATION OF INFORMATION THEORY TO DNA SEQUENCE ANALYSIS: A REVIEW

The analysis of DNA sequences through information theory methods is reviewed from the beginning in the 70s. The subject is addressed within a broad context, describing in some detail the cornerstone contributions in the field. The emerging interest concerning long-range correlations and the mosaic structure of DNA sequences is considered from our own point of view. A recent procedure developed by the authors is also outlined.

Isochore chromosome maps of the human genome

The human genome is a mosaic of isochores, which are long DNA segments (z.Gt;300 kbp) relatively homogeneous in G+C. Human isochores were first identified by density-gradient ultracentrifugation of bulk DNA, and differ in important features, e.g. genes are found predominantly in the GC-richest isochores. Here, we use a reliable segmentation method to partition the longest contigs in the human genome draft sequence into long homogeneous genome regions (LHGRs), thereby revealing the isochore structure of the human genome. The advantages of the isochore maps presented here are: (1) sequence heterogeneities at different scales are shown in the same plot; (2) pair-wise compositional differences between adjacent regions are all statistically significant; (3) isochore boundaries are accurately defined to single base pair resolution; and (4) both gradual and abrupt isochore boundaries are simultaneously revealed. Taking advantage of the wide sample of genome sequence analyzed, we investigate the correspondence between LHGRs and true human isochores revealed through DNA centrifugation. LHGRs show many of the typical isochore features, mainly size distribution, G+C range, and proportions of the isochore classes. The relative density of genes, Alu and long interspersed nuclear element repeats and the different types of single nucleotide polymorphisms on LHGRs also coincide with expectations in true isochores. Potential applications of isochore maps range from the improvement of gene-finding algorithms to the prediction of linkage disequilibrium levels in association studies between marker genes and complex traits. The coordinates for the LHGRs identified in all the contigs longer than 2 Mb in the human genome sequence are available at the online resource on isochore mapping: http://bioinfo2.ugr.es/isochores.

Prevalence of Left ventricular hypertrophy in patients with mild hypertension in primary care: Impact of echocardiography on cardiovascular risk stratification

BACKGROUND Left ventricular hypertrophy (LVH) is an important predictor of cardiovascular risk, and its detection contributes to risk stratification. The aims of the present study were to estimate the prevalence of echocardiographic LVH and to evaluate the influence of echocardiography (ECHO) on cardiovascular risk stratification in hypertensive patients presenting in primary care. METHODS In this cross-sectional study, 250 patients recently diagnosed with mild hypertension underwent clinical evaluation including electrocardiography (ECG), microalbuminuria measurement, 24-h blood pressure monitoring and ECHO. Level of cardiovascular risk was stratified, initially using routine procedures including ECG to assess target organ damage and then again after detection of LVH by ECHO. RESULTS The frequency of echocardiographic LVH was 32%, substantially higher than that detected by ECG (9%). Initial cardiovascular risk stratification yielded the following results: 30% low risk, 49% medium risk, 16% high risk, and 5% very high risk subjects. The detection of LVH by ECHO provoked a significant change in the risk strata distribution, particularly in those patients initially classified as being at medium risk. In this group, 40% of subjects were reclassified as high risk subjects according to ECHO information. The new classification was as follows: 23% low risk, 30% medium risk, 42% high risk, and 5% very high risk subjects. CONCLUSIONS A substantial proportion of mildly hypertensive patients presenting in primary care have LVH determined by ECHO. Our results suggest that this procedure could significantly improve cardiovascular risk stratification in those patients with multiple risk factors, but no evidence of target organ damage by routine investigations.