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 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 Sbisà 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.
Lanave
C
C
Centro di Studio sui Mitocondri e Metabolismo Energetico, C.N.R., Via Amendola 165/A, 70126 Bari, Italy.
Attimonelli
M
M
De Robertis
M
M
Licciulli
F
F
Liuni
S
S
Sbisá
E
E
Saccone
C
C
D000818:Animals; D004272:DNA, Mitochondrial / Q000235:genetics*; D016208:Databases, Factual; D019143:Evolution, Molecular; D016247:Information Storage and Retrieval; D020407:Internet; D009690:Nucleic Acid Conformation; D010802:Phylogeny; D012343:RNA, Transfer / Q000235:genetics; D012045:Regulatory Sequences, Nucleic Acid / Q000235:genetics; D016415:Sequence Alignment; D012984:Software; D014714:Vertebrates / Q000235:genetics
D004272:DNA, Mitochondrial; D012343:RNA, Transfer