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TIGRFAMs: a protein family resource for the functional identification of proteins

D. H. Haft
2001 Nucleic Acids Research  
TIGRFAMs is a collection of protein families featuring curated multiple sequence alignments, hidden Markov models and associated information designed to support the automated functional identification  ...  We introduce the term 'equivalog' to describe members of a set of homologous proteins that are conserved with respect to function since their last common ancestor.  ...  USING TIGRFAMs TIGRFAMs may be downloaded for use as a library of HMMs for protein identification or searched for text or sequence matches at its web site, http://www.tigr.org/TIGRFAMs.  ... 
doi:10.1093/nar/29.1.41 pmid:11125044 pmcid:PMC29844 fatcat:lvg7x3ypkja7llokui4sqtdjqi

TIGRFAMs and Genome Properties: tools for the assignment of molecular function and biological process in prokaryotic genomes

J. D. Selengut, D. H. Haft, T. Davidsen, A. Ganapathy, M. Gwinn-Giglio, W. C. Nelson, A. R. Richter, O. White
2007 Nucleic Acids Research  
Funding to pay the Open Access publication charges for this article was provided by the National Science Foundation.  ...  ACKNOWLEDGEMENTS This work has been supported by grants from the United States National Science Foundation (DBI-0445826), the United States Department of Energy (DE-FG02-04ER63935) and the United States  ...  ABSTRACT TIGRFAMs is a collection of protein family definitions built to aid in high-throughput annotation of specific protein functions.  ... 
doi:10.1093/nar/gkl1043 pmid:17151080 pmcid:PMC1781115 fatcat:aert4ty3grffblenyc65cokjfq

HMM-based databases in InterPro

A. Bateman
2002 Briefings in Bioinformatics  
Protein family databases are an important resource for protein annotation and understanding protein evolution and function.  ...  In recent years hidden Markov models (HMMs) have become one of the key technologies used for detection of members of these families.  ...  The focus of TIGRFAMs is families of proteins, especially from prokaryotes, for which function is conserved to the point that a well-informed annotator would assign the same protein name across different  ... 
doi:10.1093/bib/3.3.236 pmid:12230032 fatcat:ykxhgzgngrbblmc3zbwdrpsf7q

The Comprehensive Microbial Resource

J. D. Peterson
2001 Nucleic Acids Research  
The Comprehensive Microbial Resource (CMR) contains robust annotation of all complete microbial genomes and allows for a wide variety of data retrievals.  ...  Retrievals can be based on protein properties such as molecular weight or hydrophobicity, GC-content, functional role assignments and taxonomy.  ...  Glimmer has a ∼99% sensitivity for identification of known genes.  ... 
doi:10.1093/nar/29.1.123 pmid:11125067 pmcid:PMC29848 fatcat:nnm2poxehzaztgnexvlz4stsjq

The standard operating procedure of the DOE-JGI Microbial Genome Annotation Pipeline (MGAP v.4)

Marcel Huntemann, Natalia N. Ivanova, Konstantinos Mavromatis, H. James Tripp, David Paez-Espino, Krishnaveni Palaniappan, Ernest Szeto, Manoj Pillay, I-Min A. Chen, Amrita Pati, Torben Nielsen, Victor M. Markowitz (+1 others)
2015 Standards in Genomic Sciences  
The MGAP sequence data processing consists of feature prediction including identification of protein-coding genes, non-coding RNAs and regulatory RNA features, as well as CRISPR elements.  ...  Structural annotation is followed by assignment of protein product names and functions.  ...  Annotation consists of the identification of RNA and protein-coding genes and repeats, as well as the prediction of functions for each gene (product name assignment).  ... 
doi:10.1186/s40793-015-0077-y pmid:26512311 pmcid:PMC4623924 fatcat:7dsnixegxjfhhpmxf4xqiwy7ki

TheViral MetaGenome Annotation Pipeline (VMGAP):an automated tool for the functional annotation of viral Metagenomic shotgun sequencing data

Hernan A. Lorenzi, Jeff Hoover, Jason Inman, Todd Safford, Sean Murphy, Leonid Kagan, Shannon J. Williamson
2011 Standards in Genomic Sciences  
Here we describe a pipeline for the functional annotation of viral metagenomic sequence data.  ...  The pipeline assigns a functional term to each predicted protein sequence following a suite of comprehensive analyses whose results are ranked according to a priority rules hierarchy.  ...  Acknowledgements This research was supported by the Office of Science (BER), U.S. Department of Energy, Cooperative Agreement No.  ... 
doi:10.4056/sigs.1694706 pmid:21886867 pmcid:PMC3156399 fatcat:2kb4djzxi5h73im5xsbf7lygny

The JCVI standard operating procedure for annotating prokaryotic metagenomic shotgun sequencing data

David M. Tanenbaum, Johannes Goll, Sean Murphy, Prateek Kumar, Nikhat Zafar, Mathangi Thiagarajan, Ramana Madupu, Tanja Davidsen, Leonid Kagan, Saul Kravitz, Douglas B. Rusch, Shibu Yooseph
2010 Standards in Genomic Sciences  
The system is designed to provide the best-supported conservative functional annotation based on a combination of trusted homology-based scientific evidence and computational assertions and an annotation  ...  The JCVI metagenomics analysis pipeline provides for the efficient and consistent annotation of shotgun metagenomics sequencing data for sampling communities of prokaryotic organisms.  ...  Acknowledgements This work was performed with support from the US Department of Energy grant #DE-FG02-02ER63453, the NIH Human Microbiome Project grant #1 U54 AI84844-01, and the Gordon and Betty Moore  ... 
doi:10.4056/sigs.651139 pmid:21304707 pmcid:PMC3035284 fatcat:clitnpvpyjeg5nr5nsajnqxv3a

Improving Microbial Genome Annotations in an Integrated Database Context

I-Min A. Chen, Victor M. Markowitz, Ken Chu, Iain Anderson, Konstantinos Mavromatis, Nikos C. Kyrpides, Natalia N. Ivanova, John Parkinson
2013 PLoS ONE  
A rule based system for predicting phenotypes in IMG provides a powerful mechanism for validating functional annotations, whereby the phenotypic traits of an organism are inferred based on the presence  ...  Consistency regards the biological coherence of annotations, while completeness regards the extent and coverage of functional characterization for genomes.  ...  their contribution to the development and maintenance of the IMG systems.  ... 
doi:10.1371/journal.pone.0054859 pmid:23424620 pmcid:PMC3570495 fatcat:bio2te2hhvhjzfxufl5ej2exoi

InterPro: An integrated documentation resource for protein families, domains and functional sites

2002 Briefings in Bioinformatics  
In recognition of this, InterPro was developed as an integrated documentation resource for protein families, domains and functional sites, to rationalise the complementary efforts of the individual protein  ...  There are several signature and sequence cluster-based methods for protein classification, each resource having distinct areas of optimum application owing to the differences in the underlying analysis  ...  Acknowledgements The InterPro project is supported by the ProFuSe grant (number QLG2-CT-2000-00517) of the European Commission.  ... 
doi:10.1093/bib/3.3.225 pmid:12230031 fatcat:2igbmarmcjbpfphuwf6l7ny4cy

Genome properties in 2019: a new companion database to InterPro for the inference of complete functional attributes

Lorna J Richardson, Neil D Rawlings, Gustavo A Salazar, Alexandre Almeida, David R Haft, Gregory Ducq, Granger G Sutton, Robert D Finn
2018 Nucleic Acids Research  
To increase the scope of coverage, we have migrated GPs to function as a companion resource utilizing InterPro entries.  ...  While this provides a fine-grained view of an organism's functional protein repertoire, proteins, more commonly function in a coordinated manner, such as in pathways or multimeric complexes.  ...  ACKNOWLEDGEMENTS The authors gratefully acknowledge Peter Karp for help and support with the incorporation of MetaCyc data into Genome Properties. FUNDING  ... 
doi:10.1093/nar/gky1013 pmid:30364992 fatcat:cfganwexh5b5dhq53n2xzypxv4

Genome Properties: a system for the investigation of prokaryotic genetic content for microbiology, genome annotation and comparative genomics

D. H. Haft, J. D. Selengut, L. M. Brinkac, N. Zafar, O. White
2004 Bioinformatics  
Compiling such information across microbial genomes improves the functional classification of proteins and provides a valuable resource for comparative genomics.  ...  The results of searches using hidden Markov models allow many properties to be deduced automatically, especially for families of proteins (equivalogs) conserved in function since their last common ancestor  ...  ACKNOWLEDGEMENTS We would like to thank Tanja Davidsen for her support in integrating Genome Properties into the Comprehensive Microbial Resource.  ... 
doi:10.1093/bioinformatics/bti015 pmid:15347579 fatcat:hvu237jibrfqfdpzfnrdbqtlf4

Domains, motifs and clusters in the protein universe

Jinfeng Liu, Burkhard Rost
2003 Current Opinion in Chemical Biology  
JL and BR were supported by the grants 1-P50-GM62413-01 and RO1-GM63029-01 from the National Institute of Health (NIH).  ...  Acknowledgements Thanks to Henry Bigelow (Columbia University) for helpful comments and for critical proofreading.  ...  The corresponding upper end (too long) is given by TIGRFAMs for which the distribution is similar to that of full-length proteins [15] .  ... 
doi:10.1016/s1367-5931(02)00003-0 pmid:12547420 fatcat:3etuaqalbnbr5hxzdbajd3cdrq

The comprehensive microbial resource

Tanja Davidsen, Erin Beck, Anuradha Ganapathy, Robert Montgomery, Nikhat Zafar, Qi Yang, Ramana Madupu, Phil Goetz, Kevin Galinsky, Owen White, Granger Sutton
2009 Nucleic Acids Research  
The Comprehensive Microbial Resource or CMR (http://cmr.jcvi.org) provides a web-based central resource for the display, search and analysis of the sequence and annotation for complete and publicly available  ...  for effective mining of genomic data.  ...  ACKNOWLEDGEMENTS The authors would like to thank the J. Conflict of interest statement. None declared.  ... 
doi:10.1093/nar/gkp912 pmid:19892825 pmcid:PMC2808947 fatcat:tux7f6dqfzfljgsrmoxygjfdba

Improvement of domain-level ortholog clustering by optimizing domain-specific sum-of-pairs score

Hirokazu Chiba, Ikuo Uchiyama
2014 BMC Bioinformatics  
Identification of ortholog groups is a crucial step in comparative analysis of multiple genomes.  ...  In our method for domain-level ortholog clustering, DomClust, proteins are split into domains on the basis of alignment boundaries identified by all-against-all pairwise comparison, but it often fails  ...  Computational resources were provided by the Data Integration and Analysis Facility, National Institute for Basic Biology (NIBB), and super computer system of National Institute of Genetics (NIG), Research  ... 
doi:10.1186/1471-2105-15-148 pmid:24885064 pmcid:PMC4035852 fatcat:pe3vr23265bcpcvusze3luqfzq

The InterPro Database, 2003 brings increased coverage and new features

N. J. Mulder
2003 Nucleic Acids Research  
InterPro, an integrated documentation resource of protein families, domains and functional sites, was created in 1999 as a means of amalgamating the major protein signature databases into one comprehensive  ...  resource.  ...  This integration will enhance the capability of the database in the field of protein classification and characterisation and make the database, a true integrated resource for complete protein sequence  ... 
doi:10.1093/nar/gkg046 pmid:12520011 pmcid:PMC165493 fatcat:fy5hcc4yxvgtpgniyqtsnwmqvm
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