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JAFA: a protein function annotation meta-server
2006
Nucleic Acids Research
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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
2009
Nucleic Acids Research
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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
2007
Zenodo
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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
2007
BMC Bioinformatics
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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
2012
Journal of Structural and Functional Genomics
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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]
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 ...
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
2006
Briefings in Bioinformatics
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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
2008
Journal of Biomedical Informatics
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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
2008
Drug Discovery Today
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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
2009
Current Opinion in Structural Biology
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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
2008
PLoS ONE
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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
2008
BMC Bioinformatics
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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