1. / in a sequence name indicates that it has been seen in at least two independent studies. + at the end of a V segment sequence indicates that this sequence has been mapped (in this case the locus designation is given). All the D and J sequences in V BASE have been mapped. Further details of the aligned V BASE sequence (including the nucleotide sequence itself) can be found here.
2. The total score for each alignment corresponds to +5 for a nucleotide match and -4 for a mismatch. Germline D segments with scores over 50 would be considered to be confidently assigned. Germline D segments assignments with scores less than 50 should be treated with caution. The reading frame of the D segment is defined relative to the 5' end of the germline D segment sequence. For more information on D segment sequences and D alignments see Corbett et al. (1997). J. Mol. Biol., 270, 587-597.
3. Although the alignment parameters have been designed to find the closest germline gene, always have look at all close matches (particularly at the 3' end) to select the best assignment. Once the best match has been determined check all changes from germline against the original sequence (what appear to be somatic mutations may be the result of miscalled bases!)
4. Rearranged genes with insertions or deletions cannot be used with this software.
