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Nucleic Acids Research, Vol 27, Issue 1 134-137, Copyright © 1999 by Oxford University Press

ARTICLES

Update of AMmtDB: a database of multi-aligned metazoa mitochondrial DNA sequences

C Lanave, M Attimonelli, M De Robertis, F Licciulli, S Liuni, E Sbisa and C Saccone
Centro di Studio sui Mitocondri e Metabolismo Energetico, C.N.R., Via Amendola 165/A, 70126 Bari, Italy.

The present paper describes AMmtDB, a database collecting the multi- aligned sequences of vertebrate mitochondrial genes coding for proteins and tRNAs, as well as the multiple alignment of the mammalian mtDNA main regulatory region (D-loop) sequences. The genes coding for proteins are multi-aligned based on the translated sequences and both the nucleotide and amino acid multi-alignments are provided. As far as the genes coding for tRNAs are concerned, the multi-alignments based on the primary and the secondary structures are both provided; for the mammalian D-loop multi-alignments we report the conserved regions of the entire D-loop (CSB1, CSB2, CSB3, the central region, ETAS1 and ETAS2) as defined by Sbisa et al. [ Gene (1997), 205, 125-140). A flatfile format for AMmtDB has been designed allowing its implementation in SRS (http://bio-www.ba.cnr.it:8000/BioWWW/#AMMTDB ). Data selected through SRS can be managed using GeneDoc or other programs for the management of multi-aligned data depending on the user's operative system. The multiple alignments have been produced with CLUSTALV and PILEUP programs and then carefully optimized manually.
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