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InterProScan 5: genome-scale protein function classification
2014
Bioinformatics
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Here, we describe a new Java-based architecture for the widely used protein function prediction software package InterProScan. ...
Motivation: Robust large-scale sequence analysis is a major challenge in modern genomic science, where biologists are frequently trying to characterize many millions of sequences. ...
New to InterProScan 5 is the ability to function on a massive scale, to allow the analysis and persistence of match data for millions of sequences under the control of a single 'Master' process with a ...
doi:10.1093/bioinformatics/btu031
pmid:24451626
pmcid:PMC3998142
fatcat:kfovtogftvhpbhuwmulywlixha
IPRStats: visualization of the functional potential of an InterProScan run
2010
BMC Bioinformatics
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InterPro is a collection of protein signatures for the classification and automated annotation of proteins. ...
However, when performing whole-genome or metagenome analysis, there is a need for a fast statistical visualization of the results to have good initial grasp on the functional potential of the sequences ...
For those reasons, Interproscan [5] is a popular function annotation program. ...
doi:10.1186/1471-2105-11-s12-s13
pmid:21210980
pmcid:PMC3040527
fatcat:uhj3l6mw6nesvecjpnhcrryxum
Development of Information Biology (III)
2013
Interdisciplinary Bio Central
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The second case shows how to elucidate the function of an unknown DNA sequence or ORF in prokaryotes by a large -scale computer homology search and analyses. ...
The outcome has revealed that the cause of human cancer is located in the genome in a dormant condition. ...
The classification took a very long CPU time even by using a large-scale computer. ...
doi:10.4051/ibc.2013.5.2.0005
fatcat:f6gg4xkc6famzh77ch47dfmtl4
A biophysical approach to large-scale protein-DNA binding data
[chapter]
2008
Modern Genome Annotation
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annotation 155
5.3.1 InterProScan 155
5.3.2 Interpreting InterProScan results 156
5.3.3 Large-scale automatic annotation 159
6 From genes and proteins to genomes and proteomes 160
7 Summary 161 ...
protein signature databases 154
5.1.5 ProDom sequence clustering method 154
5.2 InterPro -integration of protein signature databases 154
5.3 Using InterProScan for sequence classification and functional ...
doi:10.1007/978-3-211-75123-7_5
fatcat:z6aywufyprdmpgs5d2xf6dmtx4
From gene expression profiling to gene regulation
[chapter]
2008
Modern Genome Annotation
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annotation 155
5.3.1 InterProScan 155
5.3.2 Interpreting InterProScan results 156
5.3.3 Large-scale automatic annotation 159
6 From genes and proteins to genomes and proteomes 160
7 Summary 161 ...
protein signature databases 154
5.1.5 ProDom sequence clustering method 154
5.2 InterPro -integration of protein signature databases 154
5.3 Using InterProScan for sequence classification and functional ...
doi:10.1007/978-3-211-75123-7_6
fatcat:qggfloahxzemrp34hqdo6s3uaa
PlantTFcat: an online plant transcription factor and transcriptional regulator categorization and analysis tool
2013
BMC Bioinformatics
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systematically analyzing InterProScan domain patterns in protein sequences. ...
Results: Here, we present PlantTFcat, a high-performance web-based analysis tool that is designed to identify and categorize plant TF/TR/CR genes from genome-scale protein and nucleic acid sequences by ...
To provide high-throughput genome-scale analysis capability, we customized InterProScan to include only relevant domain information. ...
doi:10.1186/1471-2105-14-321
pmid:24219505
pmcid:PMC4225725
fatcat:uw4xjfxfqrfnpdd6juil5tzclm
MicrobeAnnotator: a user-friendly, comprehensive functional annotation pipeline for microbial genomes
2021
BMC Bioinformatics
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Results Here, we introduce MicrobeAnnotator, a fully automated, easy-to-use pipeline for the comprehensive functional annotation of microbial genomes that combines results from several reference protein ...
Accordingly, fast and comprehensive functional gene annotation pipelines are needed to analyze and compare these genomes. ...
Acknowledgements The authors thank Luis Miguel Rodriguez for their comments and suggestions on functionality and documentation of MicrobeAnnotator. ...
doi:10.1186/s12859-020-03940-5
pmid:33407081
fatcat:vbqo3dwn2fenzceptgt4f4uggq
SECOM: A Novel Hash Seed and Community Detection Based-Approach for Genome-Scale Protein Domain Identification
2012
PLoS ONE
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The functional annotation and evolutionary history of proteins are usually inferred from domains predicted from the genome sequences. ...
Instead of conducting all-against-all sequence alignment, SECOM first indexes all the proteins in the genome by using a hash seed function. ...
Here, we propose SECOM, a powerful, novel tool that automatically identifies protein domains at a genome-wide scale. ...
doi:10.1371/journal.pone.0039475
pmid:22761802
pmcid:PMC3386278
fatcat:6szpfrjlijdz5eh4ltx7y2hh4e
LegumeIP: an integrative database for comparative genomics and transcriptomics of model legumes
2011
Nucleic Acids Research
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based on UniProt, InterProScan, Gene Ontology and the Kyoto Encyclopedia of Genes and Genomes databases. ...
We present LegumeIP (http://plantgrn.noble.org/ LegumeIP/), an integrative database for comparative genomics and transcriptomics of model legumes, for studying gene function and genome evolution in legumes ...
To better study gene function and genome evolution, two groups of putative gene families were constructed in the five species based on protein-coding sequence similarity. ...
doi:10.1093/nar/gkr939
pmid:22110036
pmcid:PMC3245131
fatcat:v4qytxzf3rexlf2djcjhraprbe
The Porcelain Crab Transcriptome and PCAD, the Porcelain Crab Microarray and Sequence Database
2010
PLoS ONE
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With the emergence of a completed genome sequence of the freshwater crustacean Daphnia pulex, construction of genomic-scale sequence databases for additional crustacean sequences are important for comparative ...
genomics and annotation. ...
some of the InterProScan homology results allow protein classification when BLAST does not. ...
doi:10.1371/journal.pone.0009327
pmid:20174471
pmcid:PMC2824831
fatcat:tg4zdfybr5a4ro4bdd6jxf45ua
Workflows for Rapid Functional Annotation of Diverse Arthropod Genomes
2021
Insects
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Genome-scale functional annotation is required for functional modeling (enrichment, networks, etc.). ...
We present an open-source, open access, and containerized pipeline for genome-scale functional annotation of insect proteomes and apply it to various arthropod species. ...
. 5 GOanna and InterProScan results for arthropod genomes selected for this study. ...
doi:10.3390/insects12080748
fatcat:2metyqt7mrbrloyllelr3swtle
The Repertoires of Ubiquitinating and Deubiquitinating Enzymes in Eukaryotic Genomes
2013
Molecular biology and evolution
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Reversible protein ubiquitination regulates virtually all known cellular activities. ...
Our method relies on a collection of profile hidden Markov models, and we demonstrate its superior performance (coverage and classification accuracy >99%) by identifying approximately 25% and approximately ...
OrthoMCL is a sensitive genome-scale algorithm for grouping orthologous protein sequences, with release 5 featuring approximately 1.4 million sequences from 150 genomes (including 57 unikonts, 13 excavates ...
doi:10.1093/molbev/mst022
pmid:23393154
pmcid:PMC3670738
fatcat:oowgk7m2cfbqtno3m35uqwyxmy
CyanoBase: the cyanobacteria genome database update 2010
2009
Nucleic Acids Research
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CyanoBase (http://genome.kazusa.or.jp/cyanobase) is the genome database for cyanobacteria, which are model organisms for photosynthesis. ...
The database houses cyanobacteria species information, complete genome sequences, genomescale experiment data, gene information, gene annotations and mutant information. ...
In addition, various genome scale experimental datasets have been produced, including gene expression profiles and protein-protein interaction data. ...
doi:10.1093/nar/gkp915
pmid:19880388
pmcid:PMC2808859
fatcat:6j2y4xhhdvhm7e547vioiobdr4
RGAugury: a pipeline for genome-wide prediction of resistance gene analogs (RGAs) in plants
2016
BMC Genomics
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A user-friendly and efficient pipeline is needed for large-scale genome-wide RGA predictions of the growing number of sequenced plant genomes. ...
Conclusions: RGAugury is an efficiently integrative bioinformatics tool for large scale genome-wide identification of RGAs. It is freely available at Bitbucket: https://bitbucket.org/yaanlpc/rgaugury. ...
Panther is a large protein database for comprehensive protein evolutionary and functional classification that contains more than 12,000 protein families from 104 sequenced genomes [45] . ...
doi:10.1186/s12864-016-3197-x
pmid:27806688
pmcid:PMC5093994
fatcat:2hwgoorznfbthl5tor7sgbsqui
Comparative genome analysis and genome evolution of members of the magnaporthaceae family of fungi
2016
BMC Genomics
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Results: A genome-scale comparative study was conducted across 74 fungal genomes to identify clusters of orthologous genes unique to the three Magnaporthaceae species as well as species specific genes. ...
No correlations between diversifying or purifying selection and distance to repetitive elements or an increased rate of evolution in secreted and small secreted proteins were observed. ...
LHO was supported by the Tri-institutional Molecular Mycology and Pathogenesis training grant (NIH 5 T32-AI052080-09 ...
doi:10.1186/s12864-016-2491-y
pmid:26911875
pmcid:PMC4766678
fatcat:wnn76vokpbfr3jwffplp4gvprq
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