Dataset Information

Using the Generic Synteny Browser (GBrowse_syn).

ABSTRACT: Genome Browsers are software that allow the user to view genome annotations in the context of a reference sequence, such as a chromosome, contig, scaffold, etc. The Generic Genome Browser (GBrowse) is an open-source genome browser package developed as part of the Generic Model Database Project (see UNIT ; Stein et al., 2002). The increasing number of sequenced genomes has led to a corresponding growth in the field of comparative genomics, which requires methods to view and compare multiple genomes. Using the same software framework as GBrowse, the Generic Synteny Browser (GBrowse_syn) allows the comparison of colinear regions of multiple genomes using the familiar GBrowse-style Web page. Like GBrowse, GBrowse_syn can be configured to display any organism, and is currently the synteny browser used for model organisms such as C. elegans (WormBase; http://www.wormbase.org; see UNIT 1.8) and Arabidopsis (TAIR; http://www.arabidopsis.org; see UNIT 1.1). GBrowse_syn is part of the GBrowse software package and can be downloaded from the Web and run on any Unix-like operating system, such as Linux, Solaris, or MacOS X. GBrowse_syn is still under active development. This unit will cover installation and configuration as part of the current stable version of GBrowse (v. 1.71).

SUBMITTER: McKay SJ

PROVIDER: S-EPMC3162311 | biostudies-literature | 2010 Sep

REPOSITORIES: biostudies-literature

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Publications

Using the Generic Synteny Browser (GBrowse_syn).

McKay Sheldon J SJ Vergara Ismael A IA Stajich Jason E JE

Current protocols in bioinformatics 20100901

Genome Browsers are software that allow the user to view genome annotations in the context of a reference sequence, such as a chromosome, contig, scaffold, etc. The Generic Genome Browser (GBrowse) is an open-source genome browser package developed as part of the Generic Model Database Project (see UNIT ; Stein et al., 2002). The increasing number of sequenced genomes has led to a corresponding growth in the field of comparative genomics, which requires methods to view and compare multiple genom ...[more]

PMID: 20836076

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Project description:BackgroundAccurate determination of orthology is central to comparative genomics. For vertebrates in particular, very large gene families, high rates of gene duplication and loss, multiple mechanisms of gene duplication, and high rates of retrotransposition all combine to make inference of orthology between genes difficult. Many methods have been developed to identify orthologous genes, mostly based upon analysis of the inferred protein sequence of the genes. More recently, methods have been proposed that use genomic context in addition to protein sequence to improve orthology assignment in vertebrates. Such methods have been most successfully implemented in fungal genomes and have long been used in prokaryotic genomes, where gene order is far less variable than in vertebrates. However, to our knowledge, no explicit comparison of synteny and sequence based definitions of orthology has been reported in vertebrates, or, more specifically, in mammals.ResultsWe test a simple method for the measurement and utilization of gene order (local synteny) in the identification of mammalian orthologs by investigating the agreement between coding sequence based orthology (Inparanoid) and local synteny based orthology. In the 5 mammalian genomes studied, 93% of the sampled inter-species pairs were found to be concordant between the two orthology methods, illustrating that local synteny is a robust substitute to coding sequence for identifying orthologs. However, 7% of pairs were found to be discordant between local synteny and Inparanoid. These cases of discordance result from evolutionary events including retrotransposition and genome rearrangements.ConclusionsBy analyzing cases of discordance between local synteny and Inparanoid we show that local synteny can distinguish between true orthologs and recent retrogenes, can resolve ambiguous many-to-many orthology relationships into one-to-one ortholog pairs, and might be used to identify cases of non-orthologous gene displacement by retroduplicated paralogs.

Project description:IntroductionA device comprising two generic earpieces with embedded dry electrodes for ear-centered electroencephalography (ear-EEG) was developed. The objective was to provide ear-EEG based sleep monitoring to a wide range of the population without tailoring the device to the individual.MethodsTo validate the device ten healthy subjects were recruited for a 12-night sleep study. The study was divided into two parts; part A comprised two nights with both ear-EEG and polysomnography (PSG), and part B comprised 10 nights using only ear-EEG. In addition to the electrophysiological measurements, subjects filled out a questionnaire after each night of sleep.ResultsThe subjects reported that the ear-EEG system was easy to use, and that the comfort was better in part B. The performance of the system was validated by comparing automatic sleep scoring based on ear-EEG with PSG-based sleep scoring performed by a professional trained sleep scorer. Cohen's kappa was used to assess the agreement between the manual and automatic sleep scorings, and the study showed an average kappa value of 0.71. The majority of the 20 recordings from part A yielded a kappa value above 0.7. The study was compared to a companioned study conducted with individualized earpieces. To compare the sleep across the two studies and two parts, 7 different sleeps metrics were calculated based on the automatic sleep scorings. The ear-EEG nights were validated through linear mixed model analysis in which the effects of equipment (individualized vs. generic earpieces), part (PSG and ear-EEG vs. only ear-EEG) and subject were investigated. We found that the subject effect was significant for all computed sleep metrics. Furthermore, the equipment did not show any statistical significant effect on any of the sleep metrics.DiscussionThese results corroborate that generic ear-EEG is a promising alternative to the gold standard PSG for sleep stage monitoring. This will allow sleep stage monitoring to be performed in a less obtrusive way and over longer periods of time, thereby enabling diagnosis and treatment of diseases with associated sleep disorders.

Dataset Information

Using the Generic Synteny Browser (GBrowse_syn).

Publications

Using the Generic Synteny Browser (GBrowse_syn).

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