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AMS 4.0: consensus prediction of post-translational modifications in protein sequences.

Amino acids | Aug 16, 2012

We present here the 2011 update of the AutoMotif Service (AMS 4.0) that predicts the wide selection of 88 different types of the single amino acid post-translational modifications (PTM) in protein sequences. The selection of experimentally confirmed modifications is acquired from the latest UniProt and Phospho.ELM databases for training. The sequence vicinity of each modified residue is represented using amino acids physico-chemical features encoded using high quality indices (HQI) obtaining by automatic clustering of known indices extracted from AAindex database. For each type of the numerical representation, the method builds the ensemble of Multi-Layer Perceptron (MLP) pattern classifiers, each optimising different objectives during the training (for example the recall, precision or area under the ROC curve (AUC)). The consensus is built using brainstorming technology, which combines multi-objective instances of machine learning algorithm, and the data fusion of different training objects representations, in order to boost the overall prediction accuracy of conserved short sequence motifs. The performance of AMS 4.0 is compared with the accuracy of previous versions, which were constructed using single machine learning methods (artificial neural networks, support vector machine). Our software improves the average AUC score of the earlier version by close to 7 % as calculated on the test datasets of all 88 PTM types. Moreover, for the selected most-difficult sequence motifs types it is able to improve the prediction performance by almost 32 %, when compared with previously used single machine learning methods. Summarising, the brainstorming consensus meta-learning methodology on the average boosts the AUC score up to around 89 %, averaged over all 88 PTM types. Detailed results for single machine learning methods and the consensus methodology are also provided, together with the comparison to previously published methods and state-of-the-art software tools. The source code and precompiled binaries of brainstorming tool are available at http://code.google.com/p/automotifserver/ under Apache 2.0 licensing.

Pubmed ID: 22555647 RIS Download

Mesh terms: Algorithms | Amino Acid Sequence | Area Under Curve | Artificial Intelligence | Consensus Sequence | Protein Processing, Post-Translational | Proteins | Sequence Analysis, Protein | Software

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Amino Acid Index Database

AAindex is a database of numerical indices representing various physicochemical and biochemical properties of amino acids and pairs of amino acids. AAindex consists of three sections now: AAindex1 for the amino acid index of 20 numerical values, AAindex2 for the amino acid mutation matrix and AAindex3 for the statistical protein contact potentials. All data are derived from published literature. An amino acid index is a set of 20 numerical values representing any of the different physicochemical and biological properties of amino acids. The AAindex1 section of the Amino Acid Index Database is a collection of published indices together with the result of cluster analysis using the correlation coefficient as the distance between two indices. This section currently contains 544 indices. Another important feature of amino acids that can be represented numerically is the similarity between amino acids. Thus, a similarity matrix, also called a mutation matrix, is a set of 210 numerical values, 20 diagonal and 20x19/2 off-diagonal elements, used for sequence alignments and similarity searches. The AAindex2 section of the Amino Acid Index Database is a collection of published amino acid mutation matrices together with the result of cluster analysis. This section currently contains 94 matrices. In the release 9.0, we added a collection of published protein pairwise contact potentials to AAindex as AAindex3. This section currently contains 47 contact potential matrices. Sponsors: This work was supported by grants and resources from the Ministry of Education, Culture, Sports, Science and Technology, and the Japan Science and Technology Agency, and the Bioinformatics Center, Institute for Chemical Research, Kyoto University and the Super Computer System, Human Genome Center, Institute of Medical Science, University of Tokyo.

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