共查询到20条相似文献,搜索用时 15 毫秒
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Background
Several protein-protein interaction studies have been performed for the yeast Saccharomyces cerevisiae using different high-throughput experimental techniques. All these results are collected in the BioGRID database and the SGD database provide detailed annotation of the different proteins. Despite the value of BioGRID for studying protein-protein interactions, there is a need for manual curation of these interactions in order to remove false positives. 相似文献3.
Background
To meet the needs of gene annotation for newly sequenced organisms, optimized spaced seeds can be implemented into cross-species sequence alignment programs to accurately align gene sequences to the genome of a related species. So far, seed performance has been tested for comparisons between closely related species, such as human and mouse, or on simulated data. As the number and variety of genomes increases, it becomes desirable to identify a small set of universal seeds that perform optimally or near-optimally on a large range of comparisons. 相似文献4.
Background
In the post-genomic era, correct gene prediction has become one of the biggest challenges in genome annotation. Improved promoter prediction methods can be one step towards developing more reliable ab initio gene prediction methods. This work presents a novel prokaryotic promoter prediction method based on DNA stability. 相似文献5.
Scott Bringans James K Hane Tammy Casey Kar-Chun Tan Richard Lipscombe Peter S Solomon Richard P Oliver 《BMC bioinformatics》2009,10(1):301
Background
Stagonospora nodorum, a fungal ascomycete in the class dothideomycetes, is a damaging pathogen of wheat. It is a model for necrotrophic fungi that cause necrotic symptoms via the interaction of multiple effector proteins with cultivar-specific receptors. A draft genome sequence and annotation was published in 2007. A second-pass gene prediction using a training set of 795 fully EST-supported genes predicted a total of 10762 version 2 nuclear-encoded genes, with an additional 5354 less reliable version 1 genes also retained. 相似文献6.
Background
Many model proteomes or "complete" sets of proteins of given organisms are now publicly available. Much effort has been invested in computational annotation of those "draft" proteomes. Motif or domain based algorithms play a pivotal role in functional classification of proteins. Employing most available computational algorithms, mainly motif or domain recognition algorithms, we set up to develop an online proteome annotation system with integrated proteome annotation data to complement existing resources. 相似文献7.
Background
A necessary step for a genome level analysis of the cellular metabolism is the in silico reconstruction of the metabolic network from genome sequences. The available methods are mainly based on the annotation of genome sequences including two successive steps, the prediction of coding sequences (CDS) and their function assignment. The annotation process takes time. The available methods often encounter difficulties when dealing with unfinished error-containing genomic sequence. 相似文献8.
Background
Since the inception of the GO annotation project, a variety of tools have been developed that support exploring and searching the GO database. In particular, a variety of tools that perform GO enrichment analysis are currently available. Most of these tools require as input a target set of genes and a background set and seek enrichment in the target set compared to the background set. A few tools also exist that support analyzing ranked lists. The latter typically rely on simulations or on union-bound correction for assigning statistical significance to the results. 相似文献9.
Peter S Klosterman Andrew V Uzilov Yuri R Bendaña Robert K Bradley Sharon Chao Carolin Kosiol Nick Goldman Ian Holmes 《BMC bioinformatics》2006,7(1):428-25
Background
Recent years have seen the emergence of genome annotation methods based on the phylo-grammar, a probabilistic model combining continuous-time Markov chains and stochastic grammars. Previously, phylo-grammars have required considerable effort to implement, limiting their adoption by computational biologists. 相似文献10.
Yohei Shinfuku Natee Sorpitiporn Masahiro Sono Chikara Furusawa Takashi Hirasawa Hiroshi Shimizu 《Microbial cell factories》2009,8(1):43
Background
In silico genome-scale metabolic models enable the analysis of the characteristics of metabolic systems of organisms. In this study, we reconstructed a genome-scale metabolic model of Corynebacterium glutamicum on the basis of genome sequence annotation and physiological data. The metabolic characteristics were analyzed using flux balance analysis (FBA), and the results of FBA were validated using data from culture experiments performed at different oxygen uptake rates. 相似文献11.
Adnane Sellam Hervé Hogues Christopher Askew Faiza Tebbji Marco van het Hoog Hugo Lavoie Carol A Kumamoto Malcolm Whiteway André Nantel 《Genome biology》2010,11(7):R71
Background
Compared to other model organisms and despite the clinical relevance of the pathogenic yeast Candida albicans, no comprehensive analysis has been done to provide experimental support of its in silico-based genome annotation. 相似文献12.
Background
In Eukaryotic genomes, different features including genes are not uniformly distributed. The integration of annotation information and genomic position of functional DNA elements in the Eukaryotic genomes opened the way to test novel hypotheses of higher order genome organization and regulation of expression. 相似文献13.
Background
Many biological processes are mediated by dynamic interactions between and among proteins. In order to interact, two proteins must co-occur spatially and temporally. As protein-protein interactions (PPIs) and subcellular location (SCL) are discovered via separate empirical approaches, PPI and SCL annotations are independent and might complement each other in helping us to understand the role of individual proteins in cellular networks. We expect reliable PPI annotations to show that proteins interacting in vivo are co-located in the same cellular compartment. Our goal here is to evaluate the potential of using PPI annotation in determining SCL of proteins in human, mouse, fly and yeast, and to identify and quantify the factors that contribute to this complementarity. 相似文献14.
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Background
Comparison of large protein datasets has become a standard task in bioinformatics. Typically researchers wish to know whether one group of proteins is significantly enriched in certain annotation attributes or sequence properties compared to another group, and whether this enrichment is statistically significant. In order to conduct such comparisons it is often required to integrate molecular sequence data and experimental information from disparate incompatible sources. While many specialized programs exist for comparisons of this kind in individual problem domains, such as expression data analysis, no generic software solution capable of addressing a wide spectrum of routine tasks in comparative proteomics is currently available. 相似文献16.
Andreas Schlicker Francisco S Domingues Jörg Rahnenführer Thomas Lengauer 《BMC bioinformatics》2006,7(1):302-16
Background
Gene Ontology (GO) is a standard vocabulary of functional terms and allows for coherent annotation of gene products. These annotations provide a basis for new methods that compare gene products regarding their molecular function and biological role. 相似文献17.
Avril Coghlan Tristan J Fiedler Sheldon J McKay Paul Flicek Todd W Harris Darin Blasiar the nGASP Consortium Lincoln D Stein 《BMC bioinformatics》2008,9(1):549
Background
While the C. elegans genome is extensively annotated, relatively little information is available for other Caenorhabditis species. The nematode genome annotation assessment project (nGASP) was launched to objectively assess the accuracy of protein-coding gene prediction software in C. elegans, and to apply this knowledge to the annotation of the genomes of four additional Caenorhabditis species and other nematodes. Seventeen groups worldwide participated in nGASP, and submitted 47 prediction sets across 10 Mb of the C. elegans genome. Predictions were compared to reference gene sets consisting of confirmed or manually curated gene models from WormBase. 相似文献18.
Background
Brucellaspecies are Gram-negative, facultative intracellular bacteria that cause brucellosis in humans and animals. Sequences of fourBrucellagenomes have been published, and variousBrucellagene and genome data and analysis resources exist. A web gateway to integrate these resources will greatly facilitateBrucellaresearch.Brucellagenome data in current databases is largely derived from computational analysis without experimental validation typically found in peer-reviewed publications. It is partially due to the lack of a literature mining and curation system able to efficiently incorporate the large amount of literature data into genome annotation. It is further hypothesized that literature-basedBrucellagene annotation would increase understanding of complicatedBrucellapathogenesis mechanisms. 相似文献19.
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