DPAAR: a Database of Perfect Amino Acid Repeat

Himansu Kumar, Swati Srivastava, Pritish Kumar Varadwaj

Abstract


Repeat of amino acids in a protein sequence has clinical and functional importance. Perfect Amino Acid Repeat (PAAR) is a kind of relational as well as flat file database which is created by the comprehensive analysis of  5,42,782 protein sequences of Swiss-Prot database (released on 19th March,2014) to know the association between repeated sequence and disease. It provides the search engine for rapid access of a particular repeated amino acid, or particular swissprot ID, or particular length of repeated amino acids in a protein sequence. It also provides the flat files for single, oligo, and tandem repeated sequence information to get the complete informaton about concerned amino acids repeat. It consists of the tables of repeated sequence and its associated disease in human being.


Keywords


Swiss-Prot database, DPAAR, repeate sequence.

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References


Miguel A. Andrade,Carolina Perez-Iratxeta,Chris P. Ponting. Protein Repeats: Structures, Functions, and Evolution. J Struct Biol. 2001 May-Jun; 134(2-3):117-31.

Szklarczyk R, Heringa J, Tracking repeats using significance and transitivity, Bioinformatics, 2004 Aug 4; 20 Suppl :i311-7.

Marcotte EM, Pellegrini M, Yeates TO, Eisenberg D. A census of protein repeats. J MolBiol, 1999, 293:151-160.

Katti MV, Sami-Subbu R, Ranjekar PK, and Gupta VS: Amino acid repeat patterns in protein sequences: Their diversity and structural-functional implications.Protein Sci 2000, 9:1203-1209.

Kalita MK, Ramasamy G, Duraisamy S, and Chauhan VS, Gupta D: ProtRepeatsDB: A database of amino acid repeats in genomes. BMC Bioinformatics, 2006, 7(1):336.

Depledge DP, Dalby AR, COPASAAR-A database for proteomic analysis of single amino acid repeats, BMC Bioinformatics 2005, 6:196.

Daniel P Depledge, Ryan PJ Lower and Deborah F Smith, RepSeq – A database of amino acid repeats present in lower eukaryotic pathogens. BMC Bioinformatics 2007, 8:122.

Karlin S, Bracchieri L, Bergman A, and Mrazek J, Gentles AJ: Amino acid runs in eukaryotic proteomes, disease associations.ProcNatlAcadSciUSA2002, 99: 333-338.