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JAFA: a protein function annotation meta-server

I. Friedberg, T. Harder, A. Godzik
2006 Nucleic Acids Research  
Here we present the Joined Assembly of Function Annotations, or JAFA server.  ...  JAFA queries several function prediction servers with a protein sequence and assembles the returned predictions in a legible, non-redundant format.  ...  JAFA is funded by NIH grant P01-GM63208. Funding to pay the Open Access publication charges for this article was provided by NIH grant P01-GM63208 and the Burnham Institute for Medical Research.  ... 
doi:10.1093/nar/gkl045 pmid:16845030 pmcid:PMC1538919 fatcat:5qhfeebt7fdtlofkwmwl3kubku

ANNIE: integrated de novo protein sequence annotation

H. S. Ooi, C. Y. Kwo, M. Wildpaner, F. L. Sirota, B. Eisenhaber, S. Maurer-Stroh, W. C. Wong, A. Schleiffer, F. Eisenhaber, G. Schneider
2009 Nucleic Acids Research  
Function prediction of proteins with computational sequence analysis requires the use of dozens of prediction tools with a bewildering range of input and output formats.  ...  functional assignments of sequence segments in the query proteins.  ...  ACKNOWLEDGEMENTS We would like to thank all colleagues that have contributed at various stages to the development of the software for protein sequence studies in the Eisenhaber group especially Georg Kraml  ... 
doi:10.1093/nar/gkp254 pmid:19389726 pmcid:PMC2703921 fatcat:i25f3afi5zcz5e5ef7776oikrm

Utmgo: A Tool For Searching A Group Of Semantically Related Gene Ontology Terms And Application To Annotation Of Anonymous Protein Sequence

Razib M. Othman, Safaai Deris, Rosli M. Illias
2007 Zenodo  
Gene Ontology terms have been actively used to annotate various protein sets. SWISS-PROT, TrEMBL, and InterPro are protein databases that are annotated according to the Gene Ontology terms.  ...  GOPET, GOtcha, GoFigure, and JAFA are used to compare the performance of the extended UTMGO.  ...  sequence as an input and then uses BLAST to predict the GO terms by identifying homologous sequences in the GO annotated databases. 5) JAFA [19] is a meta-server that uses several function prediction  ... 
doi:10.5281/zenodo.1332528 fatcat:yqbdlrahefbntjqjafjjhgrfj4

The AnnoLite and AnnoLyze programs for comparative annotation of protein structures

Marc A Marti-Renom, Andrea Rossi, Fátima Al-Shahrour, Fred P Davis, Ursula Pieper, Joaquín Dopazo, Andrej Sali
2007 BMC Bioinformatics  
Acknowledgements: This work is funded by an RO1 from the NHGRI and by a Presidential Early Career Award for Scientists and Engineers from the National Science Foundation.  ...  The motivation for creating a function prediction meta-server is twofold.  ...  We introduce a public web-server, T-FUNC, for detailed comparative analysis and functional annotation of protein structures.  ... 
doi:10.1186/1471-2105-8-s4-s4 pmid:17570147 pmcid:PMC1892083 fatcat:o5p5c46emzbhxlmq27vqibskdi

Structure- and sequence-based function prediction for non-homologous proteins

Lee Sael, Meghana Chitale, Daisuke Kihara
2012 Journal of Structural and Functional Genomics  
Two sequence-based methods, protein function prediction and extended similarity group, make use of weakly similar sequences that are conventionally discarded in homology based function annotation.  ...  In parallel effort to experimental methods, computational methods are expected to make a significant contribution for functional elucidation of such proteins.  ...  JAFA is a meta-server which combines predictions from different servers [90] . A list of more methods for sequence-based function prediction can be found in our recent articles [22, 23, 91] .  ... 
doi:10.1007/s10969-012-9126-6 pmid:22270458 pmcid:PMC3375349 fatcat:klnedt6z2bbarbldkd5vfkrsea

Automated Prediction of Protein Function from Sequence [chapter]

Meghana Chitale, Troy Hawkins, Daisuke Kihara
2008 Prediction of Protein Structures, Functions, and Interactions  
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  ...  JAFA 75 is protein function meta-server that provides joint assembly of function predictions from five different prediction servers, namely, GOFigure, 70 Gotcha, 72 Goblet, 68 InterProScan, 76  ...  any researcher to participate in annotating genes. 57 Controlled Vocabularies for Gene Function Annotation Automation of protein function prediction requires a well-established controlled vocabulary  ... 
doi:10.1002/9780470741894.ch3 fatcat:oqwctmskrre5tjg4h7atjczfxu

Automated protein function prediction--the genomic challenge

I. Friedberg
2006 Briefings in Bioinformatics  
Second, there is a need for a functional annotation which is standardized and machine readable so that function prediction programs could be incorporated into larger workflows.  ...  This is problematic due to the subjective and contextual definition of protein function. Third, there is a need to assess the quality of function predictors.  ...  Thanks to Weizhong Li for providing an advance copy of a new version of CD-HIT, used in generating the data in Figure 2 .  ... 
doi:10.1093/bib/bbl004 pmid:16772267 fatcat:br64i2dpcfeq7nmyqpfez4ru3q

A genetic similarity algorithm for searching the Gene Ontology terms and annotating anonymous protein sequences

Razib M. Othman, Safaai Deris, Rosli M. Illias
2008 Journal of Biomedical Informatics  
To show the applicability of the basic UTMGO, we extend its structure to develop a Gene Ontology -based protein sequence annotation tool named extended UTMGO.  ...  A genetic similarity algorithm is introduced in this study to find a group of semantically similar Gene Ontology terms.  ...  It uses BLAST to perform homology searches against GO-mapped protein databases, and support vector machines for the prediction and the assignment of confidence values. • JAFA [32] is a meta-server that  ... 
doi:10.1016/j.jbi.2007.05.010 pmid:17681495 fatcat:exeaidxiirat3bgi3432uiu5oi

The application of FAST-NMR for the identification of novel drug discovery targets

R POWERS, K MERCIER, J COPELAND
2008 Drug Discovery Today  
The Functional Annotation Screening Technology by NMR (FAST-NMR) screen was developed to assign a biological function for these unannotated proteins with a structure solved by the Protein Structure Initiative  ...  FAST-NMR is based on the premise that a biological function can be described by a similarity in binding sites and ligand interactions with proteins of known function.  ...  of ligand binding site for functional assignment http://ef-site.hgc.jp/eF-seek JAFA [70] Advantages • meta-server to sequence-based methods for functional annotation • does not require a structure Disadvantages  ... 
doi:10.1016/j.drudis.2007.11.001 pmid:18275915 pmcid:PMC2754198 fatcat:dznbvcxxzvgxzn6hs4y6ynk6wq

Exploiting structural classifications for function prediction: towards a domain grammar for protein function

Benoît H Dessailly, Oliver C Redfern, Alison Cuff, Christine A Orengo
2009 Current Opinion in Structural Biology  
The ability to assign function to proteins has become a major bottleneck for comprehensively understanding cellular mechanisms at the molecular level.  ...  It is also because structural data can illuminate more clearly the mechanisms by which a broader functional repertoire can emerge during evolution.  ...  Acknowledgements This work was supported by a grant from the Protein Structure Initiative (PSI) of the National Institute for General Medicine at the National Institutes of Health and by the European Union  ... 
doi:10.1016/j.sbi.2009.03.009 pmid:19398323 pmcid:PMC2920418 fatcat:4bs4xfd5nrb6hc2howuhmorjhi

De-Orphaning the Structural Proteome through Reciprocal Comparison of Evolutionarily Important Structural Features

R. Matthew Ward, Serkan Erdin, Tuan A. Tran, David M. Kristensen, Andreas Martin Lisewski, Olivier Lichtarge, Richard R. Copley
2008 PLoS ONE  
Because the number of protein structures with unknown function is mushrooming, however, we asked here whether such comparisons could be improved by focusing narrowly on the key functional features of protein  ...  to other structures; and (c) to transfer enzyme annotation whenever a plurality was reached across matches.  ...  Pooling this information can be especially useful, as shown by meta-servers such as ProFunc [84] and JAFA [97] , and by graph theoretic methods [98, 99] .  ... 
doi:10.1371/journal.pone.0002136 pmid:18461181 pmcid:PMC2362850 fatcat:frk75rt7zncgpikb2ogla25t4q

Prediction of enzyme function based on 3D templates of evolutionarily important amino acids

David M Kristensen, R Matthew Ward, Andreas Lisewski, Serkan Erdin, Brian Y Chen, Viacheslav Y Fofanov, Marek Kimmel, Lydia E Kavraki, Olivier Lichtarge
2008 BMC Bioinformatics  
In many cases (61%) a single most likely function could be predicted as the annotation with the most matches, and in these cases such a plurality vote identified the correct function with 87% accuracy.  ...  with other methods to decipher protein function in the structural proteome.  ...  Acknowledgements This work was supported in part by NSF DBI-0547695 (OL and LK) and by NIH GM066099, GM079656, and the March of Dimes MOD FY06-371 (OL), and by a Sloan Fellowship and the Brown School of  ... 
doi:10.1186/1471-2105-9-17 pmid:18190718 pmcid:PMC2219985 fatcat:mnd2blcczzc33ainjaglz4tulm