Why does VBASE2 say 'no entries found' although the sequence I pasted is holded in the database?

There may be several reasons why your sequence was not found:
A. Your sequence is longer than the VBASE2 entry. Please restrict your sequence to FR1-FR3 or use the DNAPLOT query.
B. The sequence format is not recognized. Please change it to plain sequence without line-breaks, FASTA format or use the DNAPLOT query.
C. There are one or more missmatches in the alignment of your sequence with the VBASE2 sequence. Please use the DNAPLOT query to find the corresponding VBASE2 sequence.

I have entered a V gene name in Field 1 and I have choosen 'human' in Field 2. Why do I retrieve a murine sequence as a result?

Sorry, but the Query Fields 1 - 3 must be used for seperate queries and there is no way to combine them. The query will always be performed with the values from the field where you have clicked on the query button.

Why do I get a useless DNAPLOT result without any sequence in it?

There may be several reasons why the DNAPLOT program has not recognized your sequence:
A. The FASTA head of the sequence is longer than one line in the input frame. Please shorten the headline and try again.
B. DNAPLOT may not 'find' your V gene when it has a long 5'-extension (for example, when you use the genomic sequence starting with exon1 and intron). Please shorten your sequence at the 5'-end and try again.
C.There is no V gene in your sequence - please try another one!

What means 'Unpublished' as a source reference for genomic sequence?

The genomic sequence of the heavy chain locus of the 129/Sv mouse strain is currently worked out at the GBF in the lab of Helmut Bloecker. The sequence is not yet, but will be published soon in EMBL-Bank/GenBank/DDBJ. As the sequence coverage in the assembly is 8 - 10 fold, the sequence quality is very high.

The last few nucleotides of a VBASE2 V gene are missing, although they can be found in the source reference. Why that?

This is a limitation of the automatic procedure. As the V genes may vary in length, the procedure may miss some nucleotides at the end of an exeptional long V gene. However, all efforts are done to overcome this limitation in the next version of the generation procedure.

Why there are more IMGT/LIGM references for a V gene than EMBL-Bank source references?

The source references from the EMBL-Bank are selected by the VBASE2 generation procedure. As this procedure is completely automated it needs to be very strict and requires the proper recognition of J elements and RSS sites. This limits the number of EMBL-Bank source references, whereas all IMGT/LIGM sequences with a 100% match to the V gene sequence are shown.

What means family 'na'?

'na' means 'not assigned'. Per definition, variable gene sequences that show a sequence identity of at least 80% belong to the same V gene family. The VBASE2 generation procedure aligns each V gene against a set of well established and manually edited family master (consensus) sequences. Some V genes which differ substantially from the master sequences can not be aligned properly. Thus, they cannot be assigned to a V gene family. The annotation 'na' is an evidence that this V gene is special. Many 'na' are pseudo genes or orphans.

Why there are different nomenclatures for mouse and human V gene families?

The V gene nomenclature used in the VBASE2 database refers to the respective recommendations of the genome nomenclature committees HUGO (human) and MGI (mouse).

How can I show the VBASE2 entries within the Ensembl Genome Browser?

You need to attach the human and mouse DAS sources from the DAS server at http://www.dnaplot.com/das by performing the following steps:
Go to the Ensembl website and choose a species and chromosomal position, e.g. human chromosome 14, 105500000-105900000. Scroll to the DetailedView frame. Go to the pull-down menu 'DAS Sources' and select 'Manage sources ...'. Click on 'Add DSN' and next to the field 'domain' on 'more'. Type 'www.dnaplot.com/das' into the domain field and Click on 'DSN list'. Select 'vbase2_human' to show the human VBASE2 V genes in your browser (choose 'vbase2_mouse' for depicting the mouse dataset, respectively). Click on 'next', 'next' and 'finish'. After reloading your browser the Ensembl site shows the VBASE2 V gene entries within the selected region.