Supporting data and materials for "The PFP and ESG protein function prediction methods in 2014: effect of database updates and ensemble approaches".
Dataset type: Software, Proteomic
Data released on September 15, 2015
Functional annotation of novel proteins is one of the central problems in bioinformatics. With the ever-increasing development of genome sequencing technologies, more and more sequence information is becoming available to analyze and annotate. To achieve fast and automatic function annotation, many computational (automated) function prediction (AFP) methods have been developed. To objectively evaluate the performance of such methods on a large scale, community-wide assessment experiments have been conducted. The second round of the Critical Assessment of Function Annotation (CAFA) experiment was held in 2013-2014. Evaluation of participating groups was reported in a special interest group meeting at the Intelligent Systems in Molecular Biology (ISMB) conference in Boston in 2014. Our group participated in both CAFA1 and CAFA2 using multiple, in-house AFP methods. Here, we report benchmark results of our methods obtained in the course of preparation for CAFA2 prior to submitting function predictions for CAFA2 targets.
For CAFA2, we updated the annotation databases used by our methods, protein function prediction (PFP) and extended similarity group (ESG), and benchmarked their function prediction performances using the original (older) and updated databases. Performance evaluation for PFP with different settings and ESG are discussed. We also developed two ensemble methods that combine function predictions from six independent, sequence-based AFP methods. We further analyzed the performances of our prediction methods by enriching the predictions with prior distribution of gene ontology (GO) terms. Examples of predictions by the ensemble methods are discussed.
Keywords:
Additional details
Read the peer-reviewed publication(s):
- Khan, I. K., Wei, Q., Chapman, S., KC, D. B., & Kihara, D. (2015). The PFP and ESG protein function prediction methods in 2014: effect of database updates and ensemble approaches. GigaScience, 4(1). https://doi.org/10.1186/s13742-015-0083-4
Additional information:
http://kiharalab.org/web/pfp.php
http://kiharalab.org/web/esg.php
http://bioinf.cs.ucl.ac.uk/psipred/?ffpred=1
http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE=Proteins&PROGRAM=blastp&RUN_PSIBLAST=on
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Table SettingsFile Name | Description | Sample ID | Data Type | File Format | Size | Release Date | File Attributes | Download |
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readme file describing the files included as the supplemetary material | Readme | TEXT | 1.59 kB | 2015-08-26 | MD5 checksum: 192e3706373c52878581aab6de51839e |
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File with true annotations of the benchmark dataset (2055 proteins) | Annotation | TEXT | 139.73 kB | 2015-08-26 | MD5 checksum: 005d5e5a61f610384222bb758afeaa7d |
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File with predicted annotations of the benchmark dataset by the PFP function prediction method | Annotation | TEXT | 7.10 MB | 2015-08-26 | MD5 checksum: fde3afae9134c770a04121288ba31134 |
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File with predicted annotations of the benchmark dataset by the ESG function prediction method | Annotation | TEXT | 580.25 kB | 2015-08-26 | MD5 checksum: 225a2bf4ab0dcfcfe36ed5e42c724449 |
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File with predicted annotations of the benchmark dataset by the ensemble method CONS | Annotation | TEXT | 15.84 MB | 2015-08-26 | MD5 checksum: fa4c5daa71a4b3c2149b827d9e757b89 |
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File with predicted annotations of the benchmark dataset by the ensemble method FPM | Annotation | TEXT | 361.43 kB | 2015-08-26 | MD5 checksum: d9bd1d410e80912dd485ec612f4e91bc |
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Contains AA sequence for 2055 benchmark proteins | Protein sequence | FASTA | 824.52 kB | 2015-08-26 | MD5 checksum: f32ef7877b1b76ab845ed4d038ad96dd |
Funding body | Awardee | Award ID | Comments |
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National Institute of General Medical Sciences | R01GM097528 | ||
National Science Foundation | IIS1319551 | ||
National Science Foundation | DBI1262189 | ||
National Science Foundation | DBI-0939454 | Dukka B. KC | |
National Science Foundation | IOS1127027 | ||
National Research Foundation of Korea | NRF-2011-220-C00004 |
Date | Action |
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September 24, 2015 | File Benchmark_True_Annotation.txt updated |
September 15, 2015 | Dataset publish |
September 15, 2015 | Manuscript Link added : 10.1186/s13742-015-0081-6 |
September 15, 2015 | Manuscript Link added : 10.1186/s13742-015-0083-4 |
September 24, 2015 | File CONS_pred_formatted.txt updated |
September 24, 2015 | File UniRef50_size1500_nonEmpty_annotations.fasta updated |