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ARResT/ Interrogate | SeqCure | AssignSubsets | Subsets (the Encyclopedia of CLL Subsets)

Antigen Receptors Research Tool / ARResT

ARResT is designed to enable a deep understanding of antigen receptor sequences with a cascade of algorithms and databases. ARResT, in some form or other over the years, is behind all of our publications in the field, and will continue to be in the foreseeable future. It is under constant development by and hosted at the Bioinformatics Analysis Team / BAT (i.e. us) and many colleagues and collaborators, including the ESLHO::EuroClonality-NGS Working Group on Next-Generation Sequencing for IG / TR immunoprofiling.

So far we've released some ARResT applications online, for the others please contact us - in chrono/logical order:

ARResT/SeqCure      | curating antigen receptor sequences
Based on an expandable knowledgebase and set of rules that are able to capture, describe, and advise on issues with the input sequences. This output can then be used to curate the sequences to allow for higher quality analysis.
     [server] | [citation]

ARResT/Teiresias      | discovering new subsets of stereotyped antigen receptor sequences
The pattern-based algorithm for discovering new subsets of stereotyped antigen receptor sequences, originally introduced in 2010 and behind the current 19 major subsets of stereotyped B-cell receptors in CLL. See also ARResT/AssignSubsets below.
     [code] | [citation][citation][citation][citation]

ARResT/AssignSubsets      | assigning new members to existing subsets of stereotyped antigen receptor sequences
Built to robustly assign user-submitted sequences as new members to existing subsets of stereotyped antigen receptor sequences - that implies that ARResT/AssignSubsets does not discover new subsets. This is currently applicable to the 19 major subsets of stereotyped B-cell receptors in CLL. Critically, major subsets account for >10% of the cohort, >40% of stereotyped cases, and >25% of patients requiring treatment, and seem to share clinicobiological features and, even, outcome.
     [server] | [citation]

ARResT/Subsets      | the Encyclopedia of CLL Subsets
The Encyclopedia of CLL Subsets is a unique knowledgebase on the usefully homogeneous groups of CLL patients in an otherwise heterogeneous entity. Around it, layers of novel bioinformatics solutions ensure high quality of information, and enable researchers and clinicians alike to tap into this reference resource to get insights, link their data robustly, collaborate productively.

ARResT/Interrogate      | immunoprofiling IG/TR sequence data
Web-based, interactive application for immunoprofiling IG/TR sequence data, both from NGS and Sanger. It can process, analyse, organize and filter large amounts of data by numerous criteria and their combinations, based on user-provided arbitrary metadata, and present them in the form of several interactive visualizations.
     [server] | [citation]

ARResT/Trace      | 'tracing' antigen receptor sequences
Purpose-built, ultra-sensitive, graph-based application to identify, organise and analyse all instances of user-defined or auto-detected antigen receptor sequence 'targets' - applicable to both clonality and minimal residual disease (MRD) assessment. A module of ARResT/Interrogate above, sharing all advanced functionalities such as interactivity.
     [contact us at bat@infspire.org, under development]

ARResT/CSI      | clustering antigen receptor sequences
     [contact us at bat@infspire.org, under development]