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Nucleic Acids Research, 2000, Vol. 28, No. 1 153-154
© 2000 Oxford University Press

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

Cecilia Lanave*, Sabino Liuni, Flavio Licciulli1 and Marcella Attimonelli2

Centro di Studio sui Mitocondri e Metabolismo Energetico CNR, Via Amendola 165/A, 70126 Bari, Italy, 1Area di Ricerca di Bari, CNR, Via Amendola 166/5, 70126 Bari, Italy and 2Dipartimento di Biochimica e Biologia Molecolare, Università di Bari, Via Orabona 4, 70126 Bari, Italy

Received October 4, 1999; Accepted October 6, 1999.


   ABSTRACT
TOP
 ABSTRACT
INTRODUCTION
 AMmtDB DATABASE
 CONTENT OF AMmtDB
 AVAILABILITY OF AMmtDB
 REFERENCES
 
The AMmtDB database (http://bio-www.ba.cnr.it:8000/srs6/ ) has been updated by collecting the multi-aligned sequences of Chordata mitochondrial genes coding for proteins and tRNAs. The genes coding for proteins are multi-aligned based on the translated sequences and both the nucleotide and amino acid multi-alignments are provided. AMmtDB 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. The multiple alignments have been produced with CLUSTALW and PILEUP programs and then carefully optimized manually.


   INTRODUCTION
TOP
 ABSTRACT
 INTRODUCTION
AMmtDB DATABASE
 CONTENT OF AMmtDB
 AVAILABILITY OF AMmtDB
 REFERENCES
 
Mitochondrial genomes are frequently used in molecular evolution, including molecular systematics and phylogeny studies. In Chordata, as in all Metazoa, the mitochondrial (mt) genome (1) is of circular shape, 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, the 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 needs to be met, that is, the best alignment of the sequences under comparison.

The availability of a database reporting the multi-aligned mtDNA genes associated with a system allowing the extraction and management of the selected data according to the needs of the end-users may be extremely useful.

Here we present an update of the AMmtDB database (2). The data of the previous version associated to Vertebrates, have been enriched with Agnatha and Cephalochordata, thus covering the multiple alignment for all the Chordata mt genes coding for proteins and tRNAs. Noteworthy is the section of multi-aligned D-loop sequences (3) related to mammalian species as described previously (2).


   AMmtDB DATABASE
TOP
 ABSTRACT
 INTRODUCTION
 AMmtDB DATABASE
CONTENT OF AMmtDB
 AVAILABILITY OF AMmtDB
 REFERENCES
 
Data source
Sequence data are mainly retrieved from the primary databases [EMBL (4) and GenBank (5)], generally using the ACNUC (6) retrieval system. Another source of data collection is the literature for the published sequence data not included in the primary databases. Sequences coding for partial genes are not included and only one sequence for each gene of a species has been stored.

Data organization
The database is organized into three main sections: CDS, tRNA and D-loop sequences.

The genes coding for proteins are multi-aligned on the translated sequences and both the nucleotide and amino acid multi-alignments are provided. For genes coding for tRNAs the multi-alignments based on the primary structure have been updated in the present database.

The taxonomic classes for the presently available data are: mammalian, amphibian, reptilian, aves, osteichthyes and condroi­chthyes, agnatha and cephalocordata.

The AMmtDB flat-file format (FF) has been defined and is available at http://bio-www.ba.cnr.it:8000/Tutorials/AMmtDB/AMmtDBff.html . Each entry in the FF is associated to an organism-class/gene specific multi-alignment and assumes a name composed by both the class and the gene. Cross-referencing is available to the primary databases, to the multi-alignment files and to the vertebrate MitBASE data (7).

Alignment of the data
The alignment of sequences has been performed by using different programs, CLUSTALW (8) and PILEUP (9) from the GCG package (10), and the optimization of the alignment has been performed manually by using SEAVIEW (11) and GeneDoc (12).

The present update of tRNA multi-alignments concerns the primary structure of the tRNA gene sequences. The multi-alignment based on the secondary structure of genes coding for tRNAs will be updated as soon as possible. The present release of AMmtDB reports a new multiple alignment for each gene comprehensive of all the classes listed above. Super-gene multiple alignments are no longer present in this release.


   CONTENT OF AMmtDB
TOP
 ABSTRACT
 INTRODUCTION
 AMmtDB DATABASE
 CONTENT OF AMmtDB
AVAILABILITY OF AMmtDB
 REFERENCES
 
The content of AMmtDB is schematically shown at http://bio-www.ba.cnr.it:8000/Tutorials/AMmtDB/AMMTDBTABI.html and http://bio-www.ba.cnr.it:8000/Tutorials/AMmtDB/AMMTDBTABII.html , reporting the numbers of CDS and tRNA entries, respectively, listed for the different genes and the different classes of organisms. At present, AMmtDB contains data from 916 different species: 1548 protein coding genes, 2036 tRNA genes (updated as of August 1999) and 27 mammalian D-loop.


   AVAILABILITY OF AMmtDB
TOP
 ABSTRACT
 INTRODUCTION
 AMmtDB DATABASE
 CONTENT OF AMmtDB
 AVAILABILITY OF AMmtDB
REFERENCES
 
AMmtDB can be retrieved on the WWW by using the SRS (13) server at the BioWWW site on the basis of the above described FF (http://bio-www.ba.cnr.it:8000/Tutorials/AMmtDB/AMmtDBff.html ) reporting the cross-referencing to the multi-alignment sequence files. By clicking on the file names, it is possible to display them in MSF format and/or manage them through any web browser interface with different application programs. An example of the usage of AMmtDB through SRS and GeneDoc program can be seen at http://bio-www.ba.cnr.it:8000/Tutorials/AMmtDB/example

Users of this database are kindly required to cite the present article.


   ACKNOWLEDGEMENTS
 
This work has been partially supported by MPI (Italy), by the EU-Biotechnology Programme (contract no. BIO4-CT95-0160), by ‘Programma Biotecnologie legge 95/95 (MURST 5%)’ and by CNR Research Area of Bari (Italy).


   FOOTNOTES
 
* To whom correspondence should be addressed. Tel: +39 080 548 2180; Fax: +39 080 548 4467; Email: cecilia@area.ba.cnr.it Back


   REFERENCES
TOP
 ABSTRACT
 INTRODUCTION
 AMmtDB DATABASE
 CONTENT OF AMmtDB
 AVAILABILITY OF AMmtDB
 REFERENCES
 

    1 Saccone,C. (1994) Curr. Opin. Genet. Dev., 4, 875–881.[Medline]

    2 Lanave,C., Attimonelli,M., De Robertis,M., Licciulli,F., Liuni,S., Sbisà,E. and Saccone,C. (1999) Nucleic Acids Res., 27, 134–137.[Abstract/Free Full Text]

    3 Sbisà,E., Tanzariello,F., Reyes,A., Pesole,G. and Saccone,C. (1997) Gene, 205, 125–140.[Web of Science][Medline]

    4 Stoesser,G., Tuli,M.A., Lopez,R. and Sterk,P. (1999) Nucleic Acids Res., 27, 18–24. Updated article in this issue: Nucleic Acids Res. (2000), 28, 19–23.[Abstract/Free Full Text]

    5 Benson,D.A., Boguski,M.S., Lipman,D.J., Ostell,J., Ouellette,B.F.F., Rapp,B.A. and Wheeler,D.L. (1999) Nucleic Acids Res., 27, 12–17. Updated article in this issue: Nucleic Acids Res. (2000), 28, 15–18.[Abstract/Free Full Text]

    6 Gouy,M., Gautier,C., Attimonelli,M., Lanave,C. and DiPaola,G. (1985) Comput. Appl. Biosci., 1, 167–172.[Abstract/Free Full Text]

    7 Attimonelli,M., Altamura,N., Boyen,C., Benne,R., Brennicke,A., Carone,A., Cooper,J.M., D’Elia,D., De Montalvo,A., De Pinto,B., De Robertis,M., Golik,P.J., Grienenberger,M., Knoop,V., Lanave,C., Lazowska,J., Lemagnen,A., Malladi,S., Memeo,F., Monnerot,M., Pilbout,S., Schapira,A.H.V., Sloof,P., Slonimski,P., Stevens,K. and Saccone,C. (1999) Nucleic Acids Res., 27, 128–133. Updated article in this issue: Nucleic Acids Res. (2000), 28, 148–152.[Abstract/Free Full Text]

    8 Higgins,D.G., Bleasby,A.J. and Fuchs,R. (1992) Comput. Appl. Biosci., 8, 189–191.[Abstract/Free Full Text]

    9 Higgins,D.G. and Sharp,P. (1989) Comput. Appl. Biosci., 5, 151–153.[Abstract/Free Full Text]

    10 Devereux,J., Haeberli,P. and Smithies,O. (1984) Nucleic Acids Res., 12, 387–395.

    11 Galtier,N., Gouy,M. and Gautier,C. (1996) Comput. Appl. Biosci., 12, 543–548.[Abstract/Free Full Text]

    12 Nicholas,K.B., Nicholas,H.B.,Jr and Deerfield,D.W.,II (1997) EMBnet News, 4, 14.

    13 Etzold,T., Ulyanov,A. and Argos,P. (1996) Methods Enzymol., 266, 114–128.[Web of Science][Medline]


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