Biocorpora

  • Support date format in reports for items of type DATE.

Scaligner

  • Sequences can be searched by name across all the database.
  • Sequences can be searched by subsequence across all the database.
  • Improved the similarity search: until version 3.26, only FR or CDR could be searched. Starting from this version, one can search by similarity in the V-domain (from FR1 to FR3).
  • Export aligned and antibody sequences into a FASTA file from the germline window. This functionality was already present in the alignment window, but only raw sequences could be exported from the germline window.
  • Export annotations (germline names) into a FASTA file.
  • Show germline aminoacid when hovering a mutation in the alignment window.
  • Display mutations, insertions, PTM, stop codons in the sequence window.
  • Share list with colleagues.
  • Introduction of alignment protocols to uniform the use of options for sequence import.
  • Until version 3.26, nucleotide input sequences where aligned onto the nucleotide sequence of the germline, and amino acid sequences where aligned onto the translated germline sequences. However, nucleotide sequences containing optimized codons fail to align to the nucleotide germline sequence. An new option “Germline alignment” was added to configure the alignment of sequences. When this option is set to “Align amino acid sequence”, the input sequence is translated according to the 3 reading frames in both directions, and the final alignment is the best of the 6 amino acid alignments.
  • Bugfix: until version 3.26, gaps could be introduced anywhere in a nucleotide sequence to optimize the alignment, even if frameshift correction was not activated. They were shown as X in the aligned sequence. This was necessary to align sequences that miss aminoacids. In the new release, gaps can be introduced only as triplets to prevent the creation of poorly aligned regions
  • Alignments might change when the sequence is reprocessed with new parameters. These changes are tracked in the sequence window.
  • Introduction of analysis protocols, to recall easily all the parameters for analyzing sequences

Scaligner (NGS)

  • Enable comparison of CDR3 with 3 different methods during clustering: compare CDR3 of same size only, compare CDR3 of different sizes with IMGT gaps, or with Kabat gaps. Previously, only CDR3 of the same size were compared.
  • New algorithm to analyze the diversity inside an NGS data set.