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

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 r egion (D-loop) sequences. The genes coding for proteins are multi-aligned b ased on the translated sequences and both the nucleotide and amino acid mul ti-alignments are provided. As far as the genes coding for tRNAs are concer ned, 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 regi on, ETAS1 and ETAS2) as defined by Sbisa ef al, [Gene (1997), 205, 125-140) . A flatfile format for AMmtDB has been designed allowing its implementatio n in SRS (http://bio-www.ba.cnr.it: 8000/BioWWW/#AMMTDB). Data selected thr ough SRS can be managed using GeneDoc or other programs for the management of multi-aligned data depending on the user's operative system. The multipl e alignments have been produced with CLUSTALV and PILEUP programs and then carefully optimized manually.