The Service of VBASE2
VBASE2 is an integrative database of germ-line V genes from the immunoglobulin loci of human and mouse.
It presents V gene sequences extracted from the
EMBL nucleotide sequence database and
Ensembl together with links to the
respective source sequences. Based on the properties of the source sequences, V genes are classified into 3 different classes:
| class 1 |
genomic and rearranged evidence |
| class 2 |
genomic evidence only |
| class 3 |
rearranged evidence only |
This allows careful sequence quality validation by the user.
References to other immunological databases
(KABAT,
IMGT/LIGM and
VBASE)
are given to provide all public annotation data for each V gene.
The VBASE2 database can be accessed either by the Direct Query interface or by the DNAPLOT Query interface. The Sequences given by the user are aligned with DNAPLOT against the VBASE2 database. Direct Query allows to enter sequence IDs and names (Field 1), choose species, locus, V gene family and class (Field 2) or search for 100% sequences (Field 3). At the DNAPLOT Query, a sequence given by the user is aligned with DNAPLOT against the VBASE2 database. The DNAPLOT program offers
V gene nucleotide sequence alignment referring to the
IMGT V gene unique numbering.
The Generation of VBASE2
The VBASE2 dataset is generated in an automatic process based on a
BLAST search of V genes against
the source nucleotide databases
(Ensembl,
EMBL-Bank, including
Whole Genome Shotgun (WGS) and High Throughput Genomic (HTG) sequences).
The sequences of all relevant BLAST hits are aligned against master sequences, compared and
sorted with the DNAPLOT program. V(D)J rearrangements and RSS elements are automatically detected.
The resulting germ-line V gene sequences are assigned to V gene families; the V gene family nomenclature
in VBASE2 refers to the gene nomenclature of
HUGO (human) and
MGI (mouse).
Furthermore, the V gene sequences are compared to the VBASE-, KABAT-, and IMGT/LIGM database and to a
set of germ-line V gene sequences. V gene trivial names, assigned by their discoverers, are added if any known.
The Philosophy of VBASE2
VBASE2 proceeds the VBASE sequence database regarding the aim to present germ-line sequences only and
to sort all V(D)J rearrangements by its germ-line V genes. However, VBASE2 is not manually annotated and is not limited to human V genes. It combines entries from several databases to offer an integrative access to the V gene sequence and annotation. The sequence quality
evaluation within VBASE2 is solely based on the available sequence information.
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