PROTEIN CLASSIFICATION
This research is supported by Scientific and Technical Research Council of Turkey (TUBITAK) under the project EEEAG 105E035 (2005-2007) entitled "GENOME ANNOTATION BASED ON SUBSEQUENCE ANALYSIS"
Proteins participate in every process within living cells and they have various functions
according to the process in which they participate. Therefore, it is important and useful
to determine functions of proteins in order to be able to understand the operation of organisms.
Finding out protein’s functions by wet laboratory experiments is a long, expensive and laborious
process. Instead, in silico prediction has several advantages. Although it is the three
dimensional structure that determines the function, three dimensional structure of only a few
number of proteins are known. On the other hand, sequences of all of the proteins are available
and it is now well known that conserved subsequences among different proteins are strong
indicators of functional similarity. In this project, we assume that we can extract important
information regarding to protein’s function from its sequence. We have developed representations,
algorithms and methods and implemented systems that are composed of these in order to classify
proteins according to their functions based on subsequence analysis. We have extended these
systems to annotate proteins using classification. We have generated and organized datasets
and then assessed the developed algorithms, methods and systems with these datasets and compared
the results with other methods.
Keywords: genome annotation, protein classification, function prediction,
subsequence analysis, subsequence profile
Subprojects:
Members i-cancer Research Group
- Volkan Atalay
- Rengul Atalay
- Omer Sinan Sarac, PhD candidate
- Ozge Yuzugullu, PhD candidate
- Biter Bilen, MSc
- Perit Bezek, MSc
- Gokcen Alay-Cilingir, MSc
- Ö. Sinan Saraç, Volkan Atalay, Rengül Çetin-Atalay, “Implicit Motif based Sequence Classification for Proteome Annotation”, International Symposium on Health Informatics and Bioinformatics Turkey’05, Kasım 2005, Antalya, Türkiye.
- Biter Bilen, Volkan Atalay, Mehmet Öztürk, Rengül Çetin-Atalay, “hP2SLs: a Database for Subcellular Localization of Human Proteome based on P2SL”, International Symposium on Health Informatics and Bioinformatics Turkey’05, Kasım 2005, Antalya, Türkiye ve Workshop on Emerging Topics in Human Functional Genomics and Proteomics, Mart 2006, Antalya, Türkiye.
- Ömer Sinan Saraç, Atalay, Rengül Çetin-Atalay, “HMM based Subsequence Feature Map for Proteome Classification”, Workshop on Emerging Topics in Human Functional Genomics and Proteomics, Mart 2006, Antalya, Türkiye.
- Ö. Sinan Saraç, Volkan Atalay, Rengül Çetin-Atalay, “Sınıflandırma için Protein Dizilerinin Özniteliklerinin Çıkarılmasında Model Tabanlı Yeni Bir Yöntem”, Sinyal İşleme, İletişim ve Uygulamaları Kurultayı 2006, Nisan 2006, Antalya, Türkiye.
- Ö.S. Saraç, V. Atalay, R. Çetin-Atalay, "Subsequence Feature Map for Protein Classification and Remote Homology Detection" 5th European Conference on Computational Biology (ECCB), Eliat, Israel, September 10-13, 2006 postponed to January 21-24, 2007.
- P. Bezek, Ö.S. Saraç, V. Atalay, R. Çetin-Atalay, “Protein Classification using Edit Distance based Subsequence Feature Map”, Workshop on Networks in Computational Biology, Ankara, Turkey, September 10-12, 2006.
- Ö.S. Saraç, V. Atalay, R. Çetin-Atalay, “Subsequence Feature Map for Protein Classification and Remote Homology Detection”, Max Planck-Koç Workshop on Protein Bioinformatics, September 6–8, 2006, Koç University, Istanbul, Turkey.
- Volkan Atalay, Rengül Çetin-Atalay, “Implicit motif distribution based hybrid computational kernel for sequence classification”, Max Planck-Koc Workshop on Protein Bioinformatics, September 6–8, 2006, Koç University, Istanbul, Turkey.
- Ö.S. Saraç, V. Atalay, R. Çetin-Atalay, “HMM-based subsequence feature map for Protein Classification and Remote Homology Detection”, 14th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB 2006), Forteleza, Brazil, August 6-10, 2006.
- Perit Bezek, Ö. Sinan Saraç, Volkan Atalay, Rengül Çetin-Atalay, “Spectral Clustering based Subsequence Feature Map for Protein Classification”, 11th Annual Conference on Research in Computational Biology, April 21-25, 2007, Oakland, California, USA.
- Ö. Sinan Saraç, Özge Gürsoy-Yüzügüllü, Rengül Çetin-Atalay, Volkan Atalay, “A System for Function Annotation via a Discriminative Classifier Database”, International Symposium on Health Informatics and Bioinformatics Turkey’07, April 30-May 2, Antalya, Türkiye.
- Oral Dalay, Volkan Atalay, “Finding Motifs with Maximum Density Subgraphs”, International Symposium on Health Informatics and Bioinformatics Turkey’07, April 30-May 2, Antalya, Türkiye.
- Gökçen Alay , Tolga Can and Volkan Atalay, “A Feature Mapping Technique for Protein Classification Problem Based on Frequent Patterns”, International Symposium on Health Informatics and Bioinformatics Turkey’07, April 30-May 2, Antalya, Türkiye.
- Ömer Sinan Saraç, Ö.Gürsoy-Yüzügüllü, R.Çetin-Atalay and V.Atalay, “Function Annotation via a Discriminative Classifier Database on GO hierarchy”, 15th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB 2007) and 6th European Conference Computational Biology, Vienna, Austria, July 21-25, 2007.
- Gökçen Çilingir, Tolga Can, Volkan Atalay, “Protein Classification by Feature Mapping based on Frequent Subsequences”, 15th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB 2007) and 6th European Conference Computational Biology, Vienna, Austria, July 21-25, 2007.
- Oral Dalay, Volkan Atalay, “Finding Motifs in Protein Sequences by Maximum Density Subgraphs”, 15th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB 2007) and 6th European Conference Computational Biology, Vienna, Austria, July 21-25, 2007.
- Ö.Sinan Saraç, Ö.Gürsoy-Yüzügüllü, R.Çetin-Atalay and V.Atalay, “Protein Function Annotation by Subsequence based Feature Map”, Automated Function Prediction (AFP) and Biosapiens Special Interest Group (SIG) meeting at ISMB/ECCB 2007, Vienna, Austria, July 19-20, 2007.
- Ömer Sinan Saraç, Özge Gürsoy-Yüzügüllü, Rengül Çetin-Atalay, Volkan Atalay, “Subsequence based feature map for protein function classification”, Journal of Computational Biology and Chemistry, doi:10.1016/j.compbiolchem.2007.11.004.
Theses:
- Biter Bilen, “Analyses and Web Interfaces for Protein Subcellular Localization and Gene Expression Data”, Dep. of Molecular Biology and Genetics, Bilkent University, January 2007.
- Perit Bezek, “A Clustering Method for the Problem of Protein Subcellular Localization”, Dep. of Computer Engineering, METU, January 2007.
- Gökçen Alay, “A Classification System for the Problem of Protein Subcellular Localization”, Dep. of Computer Engineering, METU, September 2007.