NAR Molecular Biology Database Collection entry number 64
Lanave C.1, Licciulli F.2, Incampo L.2, Marolla A.2, Attimonelli M.2
1Centro di Studio sui Mitocondri e Metabolismo Energetico CNR, Via Amendola 165/A, 70126 Bari, Italy
2Dipartimento di Biochimica e Biologia Molecolare, Università di Bari, Via E.Orabona 4, 70126 Bari, Italy

Database Description

Mitochondrial genomes are frequently used in molecular evolution, including molecular systematics and phylogeny studies. In Metazoa, the mitochondrial (mt) genome (1) is of circular shape; it has a genome length ranging ~16-17 kb and a very compact gene organization, i.e., no space between genes, in some cases short overlaps of genes, presence of only one major non-coding region containing, in general, the main regulatory elements. Because of its reduced size the metazoan mt genome can be completely sequenced rather easily, thus making comparative studies possible not only at the gene but also at the genomic level. For these studies a very important prerequisite is the best alignment of the sequences under comparison. The AMmtDB database compiles the Chordata and Invertebrata multi-aligned complete mitochondrial (mt) genes coding for proteins and tRNAs available from public sequence databases (updated at August 2001). These data include genes from 113 Chordata and 47 Invertebrata complete mitochondrial genomes. The genes coding for proteins are multi-aligned based on the translated sequences and both the nucleotide and aminoacid multialignments are provided. The AMmtDB database can be retrieved through SRS and is available via the web site where other mitochondrial databases developed by our group, the complete list of the sequenced mitochondrial genomes, and links to other mitochondrial sites and related information are available. Each entry in AMmtDB is related to taxonomic class specific data for the same gene. Because of the variability of the mitochondrial genomes and their usage in diversity studies, data from primary databases reporting sequences from the same species and the same genes have been analysed and grouped in gene and species specific clusters identified by a code; each cluster is stored in a multi-aligned file and the link to this file is available through the AMmtDB entries at the MV line. Further information about the variant clusters is available at the Mitochondriome Web site in the section Databases/VarMmtDB . The data selected through SRS can be viewed and managed using GeneDoc or other programs for the management of multi-aligned data depending on the user's operative system.


This work has been supported by 'Ministero Università e Ricerca Scientifica', Italy (PRIN99, Programma Biotecnologie legge 95/95-MURST 5%; Progetto MURST Cluster C03/2000, CEGBA)

Go to the abstract in the NAR 2012 Database Issue.
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