Information Technology Reference
In-Depth Information
Duprat, Bosc, Guiraudou, Jean, Ruiz, Da Piedade, Rouard, Foulquier, Thouvenin, and
Lefranc 2005b; Lefranc, Duprat, Kaas, Tranne, Thiriot, and Lefranc 2005c).
1.4.1.1 IMGT/LIGM-DB
IMGT/LIGM-DB is the comprehensive IMGT
®
database of IG and TR nucleotide
sequences from human and other vertebrate species, with translation for fully anno-
tated sequences, created in 1989 by LIGM, Montpellier, France, and available on the
Web since July 1995 (Lefranc, Giudicelli, Busin, Malik, Mougenot, Déhais, and
Chaume 1995; Giudicelli et al. 2006). In March 2007, IMGT/LIGM-DB contained
107,737 sequences of 150 vertebrate species. The unique source of data for
IMGT/LIGM-DB is EMBL (Kulikova, Aldebert, Althorpe, Baker, Bates, Browne,
van den Broek, Cochrane, Duggan, Eberhardt, Faruque, Garcia-Pastor, Harte, Kanz,
Leinonen, Lin, Lombard, Lopez, Mancuso, McHale, Nardone, Silventoinen, Stoehr,
Stoesser, Tuli, Tzouvara, Vaughan, Wu, Zhu, and Apweiler 2004) which shares data
with the other two generalist databases GenBank and DNA Data Bank of Japan
(DDBJ). Based on expert analysis, specific detailed annotations are added to IMGT
®
flat files. The Web interface allows searches according to specific immunogenetic
criteria and is easy to use without any programming language knowledge. Selection
is displayed at the top of the resulting sequences pages, so
the users can check their
own queries. Users have the possibility
to modify their request or consult the results
with a choice
of nine possibilities (Lefranc 2003; Lefranc et al. 2004b).
IMGT/LIGM-DB gene and allele name assignment and sequence annotations are
performed according to the IMGT Scientific chart rules. These annotations allow
retrieval of data from IMGT/LIGM-DB for queries in other IMGT
®
databases or
tools. As an example, the IMGT/LIGM-DB accession numbers of the cDNA ex-
pressed sequences for each human and mouse IG and TR gene are available, with
direct links to IMGT/LIGM-DB, in the IMGT/GENE-DB entries. IMGT/LIGM-DB
data are also distributed
by anonymous FTP servers at CINES (ftp://ftp.cines.fr/
IMGT/) and EBI (ftp://ftp.ebi.ac.uk/pub/databases/imgt/) and from many Sequence
Retrieval System (SRS) sites (EBI Hinxton UK, Institut Pasteur Paris, DKFZ Hei-
delberg Germany, Columbia University New York USA, IUBio Indiana University
USA, DDBJ Japan, etc.). IMGT/LIGM-DB can
be searched by BLAST or FASTA
on different servers (EBI Hinxton UK,
Institut Pasteur Paris).
1.4.1.2 IMGT/Automat for IMGT/LIGM-DB Annotations
IMGT/Automat (Giudicelli, Protat, and Lefranc 2003) is an integrated internal IMGT
®
Java tool which automatically performs the annotation of rearranged cDNA sequences
that represent half of the IMGT/LIGM-DB content. The annotation procedure includes
the IDENTIFICATION of the sequences, the CLASSIFICATION of the IG and TR
genes and alleles, and the DESCRIPTION of all IG and TR specific and constitutive
motifs within the nucleotide sequences. Accuracy and reliability of the annotation are
mainly estimated by the program itself with the evaluation of the alignment scores, the
deduced sequence functionality, and the coherence of the characterized and delimited
IG and TR motifs. So far 9890 human and mouse IG and TR cDNA sequences have
