ArticleBMC bioinformatics2005
COPASAAR--a database for proteomic analysis of single amino acid repeats.
Article in BMC bioinformatics, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed.
- Novel approach toward the understanding of genetic diversity based on the two types of amino acid repeats in Erwinia amylovora.Scientific reports · 2023Article
- The increased presence of repetitive motifs in the KDDR-plus recombinant protein, a kinesin-derived antigen from Leishmania infantum, improves the diagnostic performance of serological tests for human and canine visceral leishmaniasis.PLoS neglected tropical diseases · 2021Article
- Detection, characterization and evolutionary aspects of S54LP of SP (SAP54 Like Protein of Sesame Phyllody): a phytoplasma effector molecule associated with phyllody development in sesame (Physiology and molecular biology of plants : an international journal of functional plant biology · 2020Article
- Asparaginase treatment side-effects may be due to genes with homopolymeric Asn codons (Review-Hypothesis).International journal of molecular medicine · 2015Review
- Homepeptide repeats: implications for protein structure, function and evolution.Genomics, proteomics & bioinformatics · 2012Article
- ProRepeat: an integrated repository for studying amino acid tandem repeats in proteins.Nucleic acids research · 2012Article
- Stage-specific proteomic expression patterns of the human filarial parasite Brugia malayi and its endosymbiont Wolbachia.Proceedings of the National Academy of Sciences of the United States of America · 2011Article
- An analysis of single amino acid repeats as use case for application specific background models.BMC bioinformatics · 2011Article
- Article
- TrMADS3, a new MADS-box gene, from a perennial species Taihangia rupestris (Rosaceae) is upregulated by cold and experiences seasonal fluctuation in expression level.Development genes and evolution · 2008Article
- RepSeq--a database of amino acid repeats present in lower eukaryotic pathogens.BMC bioinformatics · 2007Article
- ProtRepeatsDB: a database of amino acid repeats in genomes.BMC bioinformatics · 2006Article
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundSingle amino acid repeats make up a significant proportion in all of the proteomes that have currently been determined. They have been shown to be functionally and medically significant, and are associated with cancers and neuro-degenerative diseases such as Huntington's Chorea, where a poly-glutamine repeat is responsible for causing the disease. The COPASAAR database is a new tool to facilitate the rapid analysis of single amino acid repeats at a proteome level. The database aims to simplify the comparison of repeat distributions between proteomes in order to provide a better understanding of their function and evolution.
resultsA comparative analysis of all proteomes in the database (currently 244) shows that single amino acid repeats account for about 12-14% of the proteome of any given species. They are more common in eukaryotes (14%) than in either archaea or bacteria (both 13%). Individual analyses of proteomes show that long single amino acid repeats (6+ residues) are much more common in the Eukaryotes and that longer repeats are usually made up of hydrophilic amino acids such as glutamine, glutamic acid, asparagine, aspartic acid and serine.
conclusionCOPASAAR is a useful tool for comparative proteomics that provides rapid access to amino acid repeat data that can be readily data-mined. The COPASAAR database can be queried at the kingdom, proteome or individual protein level. As the amount of available proteome data increases this will be increasingly important in order to automate proteome comparison. The insights gained from these studies will give a better insight into the evolution of protein sequence and function.
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