RESEARCH PAPER
A novel approach for identifying DNA repair pathways proteins using an evolutionary approach: Plasmodium falciparum case study
1
Laboratory of Bioinformatics, Institute of Molecular Biology and Biotechnology,
Adam Mickiewicz University, Poznań, Poland
2
Laboratory of Bioinformatics and Protein Engineering,
International Institute of Molecular and Cell Biology, Warszawa, Poland
3
European Center for Bioinformatics and Genomics,
Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland
Submission date: 2016-03-23
Acceptance date: 2016-10-13
Publication date: 2017-01-13
BioTechnologia 2016;97(4):245-260
KEYWORDS
TOPICS
ABSTRACT
Analysis of evolution-related proteins is one of the most effective methods for assigning functions to newly discovered proteins. We present a novel approach for identifying homologues that can be involved in DNA repair mechanisms in organisms without proteome annotation. This approach is based on the profiles built with sequences and secondary structures of proteins with known and well-described function. For this analysis, the profiles of DNA repair proteins from three model organisms (Homo sapiens, Saccharomyces cerevisiae, and Escherichia coli ) were prepared and deposited in the DNA repair pathways database – REPAIRtoire (http://repairtoire.genesilico.pl) (Milanowska et al., 2011). The methodology formulated was used to analyze all proteins from
Plasmodium falciparum and annotate those with unreviewed status that were recognized as taking part in DNA repair. The analysis identified novel proteins that have neither been previously described in the InParanoid database (O’Brien et al., 2005) as homologous or orthologous for the chosen model organisms, nor been identified by the HHsearch program (Soding, 2005). This approach is included as a search module on the REPAIRtoire website (http://repairtoire.genesilico.pl/homologs) and is available for usage.
Plasmodium falciparum and annotate those with unreviewed status that were recognized as taking part in DNA repair. The analysis identified novel proteins that have neither been previously described in the InParanoid database (O’Brien et al., 2005) as homologous or orthologous for the chosen model organisms, nor been identified by the HHsearch program (Soding, 2005). This approach is included as a search module on the REPAIRtoire website (http://repairtoire.genesilico.pl/homologs) and is available for usage.
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