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FunCat functional inference with belief propagation and feature integration
2008
Computational biology and chemistry
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innocua. hRMN consistently outperformed two competitors for annotation of four bacterial genomes. ...
We benchmarked this system with large-scale annotation transfer (based on the MIPS FunCat ontology) to proteins of the prokaryotes Bacillus subtilis, Helicobacter pylori, Listeria monocytogenes, and Listeria ...
RESULTS To benchmark hRMN for automatic functional annotation, we used a dataset of four bacterial genomes, B. subtilis, H. pylori, L. monocytogenes, and L. innocua as proposed previously (Tetko, et al ...
doi:10.1016/j.compbiolchem.2008.06.004
pmid:18684672
fatcat:asuendsynbfyzjebn5gmchcr7i
Proteome-wide protein interaction measurements of bacterial proteins of unknown function
2012
Proceedings of the National Academy of Sciences of the United States of America
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Despite the enormous proliferation of bacterial genome data, surprisingly persistent collections of bacterial proteins have resisted functional annotation. ...
In a typical genome, roughly 30% of genes have no assigned function. Many of these proteins are conserved across a large number of bacterial genomes. ...
Despite the enormous proliferation of bacterial genome data, surprisingly persistent collections of bacterial proteins have resisted functional annotation. ...
doi:10.1073/pnas.1210634110
pmid:23267104
pmcid:PMC3545810
fatcat:slas7v3ltfb67nocei7ekvepqi
FDA-ARGOS is a database with public quality-controlled reference genomes for diagnostic use and regulatory science
2019
Nature Communications
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We provide quality control metrics for the FDA-ARGOS genomic database resource and outline the need for genome quality gap filling in the public domain. ...
In the first use case, we show more accurate microbial identification of Enterococcus avium from metagenomic samples with FDA-ARGOS reference genomes compared to non-curated GenBank genomes. ...
Bacterial sequences were annotated with NCBI's Prokaryotic Genome Annotation Pipeline (PGAP) that combines ab initio gene prediction algorithms with homology-based methods. ...
doi:10.1038/s41467-019-11306-6
pmid:31346170
pmcid:PMC6658474
fatcat:ek46vv5u6rghbbt6rpfhr2vuei
Functional and structural genomics using PEDANT
2001
Bioinformatics
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There is also an acute need in reliable up-to-date genomic databases integrating both functional and structural information. ...
Results: The principal features of PEDANT are: (i) completely automatic processing of data using a wide range of bioinformatics methods, (ii) manual refinement of annotation, (iii) automatic and manual ...
This allows to conduct automatic annotation of an average size bacterial genome in just one day. ...
doi:10.1093/bioinformatics/17.1.44
pmid:11222261
fatcat:ab7kex426bguhpegx6dfhn42na
Bacterial start site prediction
1999
Nucleic Acids Research
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With the growing number of completely sequenced bacterial genes, accurate gene prediction in bacterial genomes remains an important problem. ...
These three genomes cover a broad spectrum of bacterial genomes, since B.subtilis is a Gram-positive bacterium, E.coli is a Gram-negative bacterium and P.furiosus is an archaebacterium. ...
Ladunga for helpful discussion on the MIP modeling. We also wish to thank the reviewers for many insightful remarks that helped improve the paper greatly. ...
doi:10.1093/nar/27.17.3577
pmid:10446249
pmcid:PMC148603
fatcat:ij5xsgmjiranvmbvvgcj5x5rnm
An Improved, Bias-Reduced Probabilistic Functional Gene Network of Baker's Yeast, Saccharomyces cerevisiae
2007
PLoS ONE
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Probabilistic functional gene networks are powerful theoretical frameworks for integrating heterogeneous functional genomics and proteomics data into objective models of cellular systems. ...
Such networks provide syntheses of millions of discrete experimental observations, spanning DNA microarray experiments, physical protein interactions, genetic interactions, and comparative genomics; the ...
a profile constructed only from bacterial genomes. ...
doi:10.1371/journal.pone.0000988
pmid:17912365
pmcid:PMC1991590
fatcat:qlhm3ydjzbadtoecl6wlypapay
Fast automated reconstruction of genome-scale metabolic models for microbial species and communities
2018
Nucleic Acids Research
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Starting with this universal model and annotated genome sequences, CarveMe uses a topdown approach to build single-species and community models in a fast and scalable manner. ...
Finally, we create a database of 5587 bacterial models and demonstrate its potential for fast generation of microbial community models. ...
ACKNOWLEDGEMENTS The authors would like to thank Jaime Huerta-Cepas for implementing support for BiGG annotations in eggnogmapper and Markus Herrgård for critical comments on the manuscript. ...
doi:10.1093/nar/gky537
pmid:30192979
pmcid:PMC6125623
fatcat:edtdezpjkndbna2oj43vzahp3e
Comparative evolutionary analysis of protein complexes in E. coli and yeast
2010
BMC Genomics
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Furthermore, such complexes are involved in eukaryotic-specific functions. ...
Results: We generated accurate, high coverage datasets of protein complexes for E. coli and yeast in order to study differences in the evolution of complexes between these two species. ...
These complex datasets thus covered roughly 56%, and 85% of E. coli and yeast genomes respectively based on genome sizes of 3952 and 5586 genes (genome sizes were taken from Integr8 [42] ). ...
doi:10.1186/1471-2164-11-79
pmid:20122144
pmcid:PMC2837643
fatcat:7vn5arol5ba4nlotp7itcvumyi
WheatNet: a Genome-Scale Functional Network for Hexaploid Bread Wheat, Triticum aestivum
2017
Molecular Plant
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Sequencing Consortium MIPS annotation version 2.2. ...
Benchmarking inferred functional linkages between wheat genes Various types of genomics data were analyzed to infer functional associations between wheat genes by using supervised machine learning, which ...
doi:10.1016/j.molp.2017.04.006
pmid:28450181
fatcat:sxpesz5bqngrpc2jenunx3thwu
Automated Prediction of Protein Function from Sequence
[chapter]
2008
Prediction of Protein Structures, Functions, and Interactions
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Comparative genomics approaches FRpred 128 http://toolkit.tuebingen.mpg.de/frpred Prediction of protein functional residues MINER 120 http://coit-apple01.uncc.edu/MINER/ Functional residue prediction PSORT ...
dataset. ...
Thus, homology-based function prediction is still needed for the starting point of a genome scale annotation. ...
doi:10.1002/9780470741894.ch3
fatcat:oqwctmskrre5tjg4h7atjczfxu
WheatNet: A genome-scale functional network for hexaploid bread wheat, Triticum aestivum
[article]
2017
bioRxiv
pre-print
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WheatNet was constructed by integrating 20 distinct genomics datasets, including 156,000 wheat-specific co-expression links mined from 1,929 microarray data. ...
Here we report the generation of WheatNet, the first genome-scale functional network for T. aestivum and a companion web server (www.inetbio.org/wheatnet). ...
Sequencing Consortium MIPS annotation version 2.2. ...
doi:10.1101/105098
fatcat:kkg5ly434nhsbdrdiljynqm6le
KEA3: improved kinase enrichment analysis via data integration
2021
Nucleic Acids Research
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To benchmark the performance of KEA3, we examined whether KEA3 can predict the perturbed kinase from single-kinase perturbation followed by gene expression experiments, and phosphoproteomics data collected ...
The KinCREEDSupdn benchmark dataset consists of gene sets extracted from 329 kinase loss-of-function/gain-of-function (LOF/GOF) human and mouse microarray experiments mined from GEO by contributors to ...
We term this benchmarking dataset KinCREEDSupdn. ...
doi:10.1093/nar/gkab359
pmid:34019655
pmcid:PMC8265130
fatcat:gru3qfwaofbnvpd33jgy3nlh2e
A Domain Interaction Map Based on Phylogenetic Profiling
2004
Journal of Molecular Biology
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Phylogenetic profiling is a well established method for predicting functional relations and physical interactions between proteins. ...
The resulting domain interaction map (DIMA) can be explored directly or mapped to a genome of interest. ...
Table 3 . 3 Accuracy of functional-link prediction evaluated against the MIPS FUNCAT annotation Sample size
Sensitivity
Specificity
NPV
PPV
Dataset
Pairs
Proteins
DIMA
CLASSIC
DIMA
CLASSIC ...
doi:10.1016/j.jmb.2004.10.019
pmid:15561146
fatcat:cdaccsjknncd5jnk7yw6lx75eu
Fast automated reconstruction of genome-scale metabolic models for microbial species and communities
[article]
2018
bioRxiv
pre-print
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Starting with this universal model and annotated genome sequences, CarveMe uses a top-down approach to build single-species and community models in a fast and scalable manner. ...
Finally, we demonstrate the scalability of CarveMe through reconstructing 5587 bacterial models. ...
Thus, applications of metabolic modeling lag behind the opportunities presented by the increasing number of genomics and metagenomics datasets [19] . ...
doi:10.1101/223198
fatcat:vnwdx3ad35a2zoy3bncx5gxwgu
Genome-enabled insights into the biology of thrips as crop pests
2020
BMC Biology
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Benchmarking Universal Single-Copy Ortholog (BUSCO) assessments of the genome assembly (size = 415.8 Mb, scaffold N50 = 948.9 kb) revealed a relatively complete and well-annotated assembly in comparison ...
Our study also offers a genomic benchmark for molecular and evolutionary investigations of other Thysanoptera species. ...
Acknowledgements We thank the staff at the Baylor College of Medicine Human Genome Sequencing Center for their contributions. ...
doi:10.1186/s12915-020-00862-9
pmid:33070780
fatcat:zqqwcbvquffu3jelq6rzxhtkne
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