Abstract
Amino acid repeats are found to play important roles in both structures and functions of the proteins. These are commonly found in all kingdoms of life, especially in eukaryotes and a larger fraction of human proteins composed of repeats. Further, the abnormal expansions of shorter repeats cause various diseases to humans. Therefore, the analysis of repeats of the entire human proteome along with functional, mutational and disease information would help to better understand their roles in proteins. To fulfill this need, we developed a web database HPREP (http://bioinfo.bdu.ac.in/hprep) for human proteome repeats using Perl and HTML programming. We identified different categories of well-characterized repeats and domain repeats that are present in the human proteome of UniProtKB/Swiss-Prot by using in-house Perl programming and novel repeats by using the repeat detection T-REKS tool as well as XSTREAM web server. Further, these proteins are annotated with functional, mutational and disease information and grouped according to specific repeat types. The developed database enables the users to search by specific repeat type in order to understand their involvement in proteins. Thus, the HPREP database is expected to be a useful resource to gain better insight regarding the different repeats in human proteome and their biological roles.
Highlights
Amino acid repeats that are commonly found in all kingdoms of life have played essential roles on both structures and functions of the proteins [1]
We developed a web database HPREP for human proteome repeats using Perl and HTML programming
We identified different categories of well-characterized repeats and domain repeats that are present in the human proteome of UniProtKB/Swiss-Prot by using in-house Perl programming and novel repeats by using the repeat detection T-REKS tool as well as XSTREAM web server
Summary
Amino acid repeats that are commonly found in all kingdoms of life have played essential roles on both structures and functions of the proteins [1]. The roles played by the domain repeats of immunoglobulin, human matrix metalloproteinase and zinc finger type proteins in protein–protein interaction as well as binding to DNA or RNA have been observed [6,7,8]. The repeats in the sequences of Protein Data Bank (PDB) [14] and UniProtKB/Swiss-Prot [15] identified by using RADAR have been analyzed at the structural and functional level. Several databases for amino acid repeats from different set of protein sequences were constructed for large scale analysis. The PRDB includes repeats found in the sequences of (i) NR (non-redundant) data bank of NCBI (ii) PDB and (iii) Swiss-Prot obtained by using T-REKS program [18].
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