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Clustering

The alignment window provides the capability to group sequences identical on some regions, or to sort by similarity compared to a given sequence. Clustering extends this functionality by the creation of clusters based on similarity threshold, and not only on sequence identity. Select the CDR definition, the regions and the similarity level, and Scaligner will […]

Humanness evaluation

Scaligner implements several scores to evaluate the humanness of a sequence: H-score: expressed human antibody sequences from the latest Kabat database (2000) have been grouped by isotype (IGHV, IGKV, IGLV). The ‘raw humanness’  of an antibody variable domain is defined as the mean sequence identity of a variable region sequence scored against all distinct human […]

Analyze next generation sequencing data

Based on the sequence-based discovery platform described in the paper of Trinklein et al, Scaligner has been used to analyze NGS data. OmniFlic rats have been immunized, and lymphocytes from relevant draining lymph nodes were harvested. Samples were sequenced, leading to 1 million DNA sequences for each samples on average. Framework regions of the VH […]

Archive sequences in an in-house repository

Scaligner is not only a sequence alignment and analysis tool. It also gives to researchers the ability to keep sequences in a long-term, secure database. Organize sequences Scaligner enables scientists to organize sequences in lists to preserve the project’s history and to facilitate a comprehensive review of your data. On-demand access to sequence is granted […]

Visualize sequence alignments

Once sequences have been analyzed, alignments can be displayed to the alignment window. For each sequence, CDRs and framework regions are displayed using user-defined templates and rules, and the sequence is annotated. The interface provides many key facilities including: Highlight mutations, frameshifts, Highlight sites of potential post-translational modification and STOP codons Cluster sequences by region: […]

Share sequence annotations

The sequence window gathers all the information available about a sequence. Sequences The introduction consists in the the sequence of the antibody. The raw sequence is the sequence imported in Scaligner. It might contain a leader sequence, a linker, a tail and so on. It might DNA or protein sequence. The antibody sequence is the […]

Automate sequence analysis

Sequences are imported one by one or in batch from FASTA files, and are aligned automatically onto a set of germlines to identify the closest match. The list of germlines is stored in the database and Scaligner can therefore handle virtually any species. During the analysis, light and heavy chains are detected automatically in the […]