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  • Wesley C Warren, David F Clayton, Hans Ellegren, Arthur P Arnold, Ladeana W Hillier, Axel Künstner +76 others
  • 2010
The zebra finch is an important model organism in several fields with unique relevance to human neuroscience. Like other songbirds, the zebra finch communicates through learned vocalizations, an ability otherwise documented only in humans and a few other animals and lacking in the chicken-the only bird with a sequenced genome until now. Here we present a(More)
Alternative splicing, polyadenylation of pre-messenger RNA molecules and differential promoter usage can produce a variety of transcript isoforms whose respective expression levels are regulated in time and space, thus contributing specific biological functions. However, the repertoire of mammalian alternative transcripts and their regulation are still(More)
The problem of extracting from a set of nucleic acid sequences motifs which may have biological function is more and more important. In this paper, we are interested in particular motifs that may be implicated in the transcription process. These motifs, called structured motifs, are composed of two ordered parts separated by a variable distance and allowing(More)
UNLABELLED Massive parallel sequencing has revolutionized the search for pathogenic variants in the human genome, but for routine diagnosis, re-sequencing of the complete human genome in a large cohort of patients is still far too expensive. Recently, novel genome partitioning methods have been developed that allow to target re-sequencing to specific(More)
MOTIVATION Automatic error correction of high-throughput sequencing data can have a dramatic impact on the amount of usable base pairs and their quality. It has been shown that the performance of tasks such as de novo genome assembly and SNP calling can be dramatically improved after read error correction. While a large number of methods specialized for(More)
SUMMARY The seq++ package offers a reference set of programs and an extensible library to biologists and developers working on sequence statistics. Its generality arises from the ability to handle sequences described with any alphabet (nucleotides, amino acids, codons and others). seq++ enables sequence modelling with various types of Markov models,(More)
MOTIVATION The detection of structural variations (SVs) in short-range Paired-End (PE) libraries remains challenging because SV breakpoints can involve large dispersed repeated sequences, or carry inherent complexity, hardly resolvable with classical PE sequencing data. In contrast, large insert-size sequencing libraries (Mate-Pair libraries) provide higher(More)
The web software SIC provides a tool to search for short inverted segments (length 3-5000 bp) in a DNA sequence. The sequence is assumed to follow a Markov model. A statistic which is sensitive to inversion is presented. Searching inverted segments is done by a scanning approach after the user specifies the size of the scanning window and the order of the(More)
BACKGROUND Patterns of care for acute myocardial infarction (AMI) strongly depend on the availability of on-site cardiac catheterization facilities. Although the management found at hospitals without on-site catheterization does not lead to increased mortality, little it known about its impact on resource utilization and non-fatal outcomes. METHODS We(More)
Many statistical methods and programs are available to compute the significance of a given DNA pattern in a genome sequence. In this paper, after outlining the mathematical background of this problem, we present SPA (Statistic for PAtterns), an expert system with a simple web interface designed to be applied to two of these methods (large deviation(More)