Automate sequence alignments. Perform pairwise (or multiple) sequence alignments to determine the relatedness of a pair (or a mutiple) of sequences, e.g the sequence of an uncharacterized immunoglobulin sequence to the sequence of a related reference sequence or germline sequence, all within the same interface you use for post-alignment analysis.
Scaligner™ makes it easy to further explore the relatedness of pairs of sequences from multiple alignments, align transcripts to genes, or find a gene within a genome.
The reliable assignment of rearranged immunoglobulin genes to their respective germline alleles is an important first step in the analysis of antibody repertoires, to determine germline gene usage, as well as to help characterize clonotypes within the repertoire.
Visualize frameshifts, mutations, post-translational modifications and stop codons by color-code. Scaligner™ identifies mutations, and patterns in sequences such as potential post-translational modification sites and stop codons during the automated analysis process. Mutations, PTMs and stop codons are highlighted by color and are immediately recognized.
Cluster sequences by selected CDRs or framework regions. Sort your sequences by the region of interest (e.g. CDR or framework region). Scaligner™’s built-in sequence similarity computation tool identifies “homologous” proteins by comparing amino acids at equivalent positions according to the numbering scheme and groups those sequences into clusters.