Nucleic Acids Research Advance Access originally published online on December 6, 2006
Nucleic Acids Research 2007 35(Database issue):D431-D438; doi:10.1093/nar/gkl1039
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Nucleic Acids Research, 2007, Vol. 35, Database issue D431-D438
© 2006 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
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Comparasite: a database for comparative study of transcriptomes of parasites defined by full-length cDNAs
Department of Parasitology, Institute of Medical Science, Graduate School of Frontier Sciences, University of Tokyo 4-6-1, Shirokanedai, Minatoku, Tokyo 108-8639, Japan 1 Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo 4-6-1, Shirokanedai, Minatoku, Tokyo 108-8639, Japan
*To whom correspondence should be addressed. Tel: +81 3 5689 3979; Fax: +81 3 5689 3979; Email: jwatanab{at}ims.u-tokyo.ac.jp
Received August 15, 2006. Revised November 2, 2006. Accepted November 3, 2006.
Comparasite is a database for comparative studies of transcriptomes of parasites. In this database, each data is defined by the full-length cDNAs from various apicomplexan parasites. It integrates seven individual databases, Full-Parasites, consisting of numerous full-length cDNA clones that we have produced and sequenced: 12 484 cDNA sequences from Plasmodium falciparum, 11 262 from Plasmodium yoelii, 9633 from Plasmodium vivax, 1518 from Plasmodium berghei, 7400 from Toxoplasma gondii, 5921 from Cryptosporidium parvum and 10 966 from the tapeworm Echinococcus multilocularis. Putatively counterpart gene groups are clustered and comparative analysis of any combination of six apicomplexa species is implemented, such as interspecies comparisons regarding protein motifs (InterPro), predicted subcellular localization signals (PSORT), transmembrane regions (SOSUI) or upstream promoter elements. By specifying keywords and other search conditions, Comparasite retrieves putative counterpart gene groups containing a given feature in common or in a species-specific manner. By enabling multi-faceted comparative analyses of genes of apicomplexa protozoa, monophyletic organisms that have evolved to diversify to parasitize various hosts by adopting complex life cycles, Comparasite should help elucidate the mechanism behind parasitism. Our full-length cDNA databases and Comparasite are accessible from http://fullmal.ims.u-tokyo.ac.jp.
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