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BIOINFORMATICS MIPS Bacterial Genomes Functional Annotation Benchmark Dataset

by Igor V. Tetko, Barbara Brauner, Irmtraud Dunger-kaltenbach, Corinna Montrone, Gisela Fobo, Alexey V, Dimitrij Surmeli, Hans W. Mewes
"... Motivation: Any development of new methods for automatic functional annotation of proteins according to their se-quences requires high-quality data (as benchmark) as well as tedious preparatory work to generate sequence parame-ters required as input data for the machine learning meth-ods. Different ..."
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program settings and incompatible protocols make a comparison of the analyzed methods difficult. Results: The MIPS Bacterial Functional Annotation Bench-mark data set (MIPS-BFAB) is a new high-quality resource comprising four bacterial genomes manually annotated ac-cording to the MIPS Functional Catalogue

BIOINFORMATICS APPLICATIONS NOTE

by Genome Analysis, Igor V. Tetko, Barbara Brauner, Irmtraud Dunger-kaltenbach, Goar Frishman, Corinna Montrone, Gisela Fobo, Alexey V. Antonov, Dimitrij Surmeli , 2005
"... doi:10.1093/bioinformatics/bti380 MIPS bacterial genomes functional annotation benchmark dataset ..."
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doi:10.1093/bioinformatics/bti380 MIPS bacterial genomes functional annotation benchmark dataset

genomes

by Vetriselvi Rangannan, Manju Bansal, Martin Bishop , 2010
"... Motivation: The number of bacterial genomes being sequenced is increasing very rapidly and hence, it is crucial to have procedures for rapid and reliable annotation of their functional elements such as promoter regions, which control the expression of each gene or each transcription unit of the geno ..."
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Motivation: The number of bacterial genomes being sequenced is increasing very rapidly and hence, it is crucial to have procedures for rapid and reliable annotation of their functional elements such as promoter regions, which control the expression of each gene or each transcription unit

A Phylogeny-Based Benchmarking Test for Orthology Inference Reveals the Limitations of Function-Based Validation

by Kalliopi Trachana, Kristoffer Forslund, Tomas Larsson, Sean Powell, Tobias Doerks, Christian Von Mering, Peer Bork
"... Accurate orthology prediction is crucial for many applications in the post-genomic era. The lack of broadly accepted benchmark tests precludes a comprehensive analysis of orthology inference. So far, functional annotation between orthologs serves as a performance proxy. However, this violates the fu ..."
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Accurate orthology prediction is crucial for many applications in the post-genomic era. The lack of broadly accepted benchmark tests precludes a comprehensive analysis of orthology inference. So far, functional annotation between orthologs serves as a performance proxy. However, this violates

Annotation of metagenome short reads using proxygenes. Bioinformatics 24: i7-i13

by Daniel Dalevi, Natalia N. Ivanova, Konstantinos Mavromatis, Sean D. Hooper, Ernest Szeto, Philip Hugenholtz, Nikos C. Kyrpides, Victor M. Markowitz - Ivanova NN, Mavromatis K, Hooper SD, Szeto E, Hugenholtz P, Kyrpides NC, and 570 Markowitz VM , 2008
"... Motivation: A typical metagenome dataset generated using a 454 pyrosequencing platform consists of short reads sampled from the collective genome of a microbial community. The amount of sequence in such datasets is usually insufficient for assembly, and traditional gene prediction cannot be applied ..."
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datasets as benchmarks, we show that the proxygene method is more accurate than the direct assignment. We introduce a clustering method which significantly reduces the size of a metagenome dataset while maintaining a faithful representation of its functional and taxonomic content. Contact:

Defining the Estimated Core Genome of Bacterial Populations Using a Bayesian Decision Model

by Andries J. Van Tonder, Shilan Mistry, James E. Bray, Dorothea M. C. Hill, Alison J. Cody, Chris L. Farmer, Keith P. Klugman, Anne Von Gottberg, Stephen D. Bentley, Julian Parkhill, Keith A. Jolley, Martin C. J. Maiden, Angela B. Brueggemann
"... The bacterial core genome is of intense interest and the volume of whole genome sequence data in the public domain available to investigate it has increased dramatically. The aim of our study was to develop a model to estimate the bacterial core genome from next-generation whole genome sequencing da ..."
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data and use this model to identify novel genes associated with important biological functions. Five bacterial datasets were analysed, comprising 2096 genomes in total. We developed a Bayesian decision model to estimate the number of core genes, calculated pairwise evolutionary distances (p

Sequence analysis Beyond the “Best ” Match: Machine Learning Annotation of Protein Sequences by Integration of Different Sources of Information

by Igor V. Tetko, Igor V. Rodchenkov, Mathias C. Walter
"... Accurate automatic assignment of protein functions remains a chal-lenge for genome annotation. We have developed and compared the automatic annotation of four bacterial genomes employing a 5-fold cross-validation procedure and several machine learning meth-ods. The analyzed genomes were manually ann ..."
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Accurate automatic assignment of protein functions remains a chal-lenge for genome annotation. We have developed and compared the automatic annotation of four bacterial genomes employing a 5-fold cross-validation procedure and several machine learning meth-ods. The analyzed genomes were manually

doi:10.1093/nar/gkm597 A survey of bacterial insertion sequences using IScan

by Andreas Wagner, Christopher Lewis, Manuel Bichsel , 2007
"... Bacterial insertion sequences (ISs) are the simplest kinds of bacterial mobile DNA. Evolutionary studies need consistent IS annotation across many different genomes. We have developed an open-source soft-ware package, IScan, to identify bacterial ISs and their sequence elements—inverted and target d ..."
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Bacterial insertion sequences (ISs) are the simplest kinds of bacterial mobile DNA. Evolutionary studies need consistent IS annotation across many different genomes. We have developed an open-source soft-ware package, IScan, to identify bacterial ISs and their sequence elements—inverted and target

Improved sensitivity and reliability of anchor based genome alignment

by Raluca Uricaru, Celia Michotey, Laurent Noé, Hélène Chiapello, Eric Rivals - PROCEEDINGS OF THE 10TH OPEN DAYS IN BIOLOGY, COMPUTER SCIENCE AND MATHEMATICS (JOBIM) , 2009
"... Whole genome alignment is a challenging problem in computational comparative genomics. It is essential for the functional annotation of genomes, the understanding of their evolution, and for phylogenomics. Many global alignment programs are heuristic variations on the anchor based strategy, which re ..."
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Whole genome alignment is a challenging problem in computational comparative genomics. It is essential for the functional annotation of genomes, the understanding of their evolution, and for phylogenomics. Many global alignment programs are heuristic variations on the anchor based strategy, which

Protein Function Prediction via Laplacian Network Partitioning Incorporating Function Category Correlations

by Hua Wang, Heng Huang, Chris Ding - PROCEEDINGS OF THE TWENTY-THIRD INTERNATIONAL JOINT CONFERENCE ON ARTIFICIAL INTELLIGENCE
"... Understanding the molecular mechanisms of life requires decoding the functions of the proteins in an organism. Various high-throughput experimental techniques have been developed to characterize biological systems at the genome scale. A fundamental challenge of the post-genomic era is to assign biol ..."
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GRID dataset for the Saccharomyces Cerevisiae species using the MIPS annotation scheme. Our new method outperforms other related state-of-the-art approaches more than 63 % by the average precision of function prediction and 53% by the average F1 score.
Results 1 - 10 of 31