citation and acknowledgements
ARResT/SeqCure was published as part of ARResT/AssignSubsets in Bioinformatics:
ARResT/AssignSubsets: a novel application for robust subclassification of chronic lymphocytic leukemia based on B cell receptor IG stereotypy
Vojtech Bystry; Andreas Agathangelidis; Vasilis Bikos; Lesley Ann Sutton; Panagiotis Baliakas; Anastasia Hadzidimitriou; Kostas Stamatopoulos; Nikos Darzentas
Bioinformatics 2015
doi: 10.1093/bioinformatics/btv456
| acknowledgements
We acknowledge the influence of Chrysoula Belessi and Kostas Stamatopoulos on our work, as well as Fred Davi, Paolo Ghia, and Richard Rosenquist – all founding members of the IgCLL group. We also acknowledge IMGT® for close collaboration, all other members of the ERIC expert review board, and numerous colleagues and collaborators from over the years. Finally, we acknowledge support from Sarka Pospisilova and the Medical Genomics Group at CEITEC MU.
This work has been supported by CEITEC MU (CZ.1.05/1.1.00/02.0068), SYLICA (FP7-REGPOT-2011-1), and SuPReMMe (CZ.1.07/2.3.00/20.0045); the Nordic Cancer Union, the Swedish Cancer Society, the Swedish Research Council, and the Lion’s Cancer Research Foundation, Uppsala; Associazione Italiana per la Ricerca sul Cancro AIRC (Special Program Molecular Clinical Oncology – 5 per mille #9965); the Hellenic General Secretariat for Research and Technology (GSRT).
The tool is currently supported by Ministry of Health of the Czech Republic grant nr. 16-34272A.
news and updates
29.06.23 | 100% identity to germline was (unintentionally) reported as 0.00% in the SeqCure report, didn't affect anything else AFAIK
07.01.22 | fix for IMGT switching to https
10.11.19 | improvement for sequence labels with tabs, mainly affecting ARResT/AssignSubsets
28.08.19 | fix for IMGT/V-QUEST 3.5.8
26.07.19 | quick response from IMGT, we should be back to normal
26.07.19 | temporary fix for IMGT/V-QUEST 3.5.3 and its modified API; we're missing IMGT's run parameters, shouldn't affect results, but report any issues
29.05.19 | update for IMGT/V-QUEST 3.5.0 and its new API; shouldn't affect results, but please report any issues
11.10.18 | fix for handling of problematic sequences
29.06.18 | improvements in handling problematic sequences and feedback to user (thanks to Elisa Pagnin for the motivation)
14.02.18 | underlying code has been rewritten and software (e.g. R) updated, so please report any issues you might encounter
17.07.17 | functionality and its comments were not properly used due to header changes in IMGT/V-QUEST 3.4.6 (30 March 2017)
10.10.15 | timeout issue with long runs should be resolved - apologies for any downtime or erroneous ("no (healthy) data...") runs, please repeat if unsure
16.03.15 | online
background and instructions
| intro
ARResT/SeqCure is 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.
| input formats
Input is antigen receptor nucleotide sequences, in either FASTA format or tab-delimited. Sequence ID will be cut at first ';' (and still finally truncated to 49 characters at IMGT)
>ID1 acgtacgtacgt >ID2 cgtacgtacgta-or-
ID1[tab]acgtacgtacgt ID2[tab]cgtacgtacgta
We have enabled the use of the tab key in the textbox above, but the tab-delimited format is mainly provided for simply copy-pasting such information from a spreadsheet (e.g. Excel).
| progress
When you are ready click on 'submit to ARResT/SeqCure'. The page will change to keep you informed of our progress. This includes a preliminary table of colour-coded alarm levels and counts of issues with your sequences (more on this below). ARResT/SeqCure has two main stages which again you can follow here, primary and advanced, the latter based on running IMGT/V-QUEST, twice if necessary to confirm a potential insertion or deletion (indel). In the end, provided that everything went smoothly, you will be provided with a link to see the full report.
| output / report
The report section provides messages generated by ARResT/SeqCure, including the sequence ID and index/order (from zero) and the stage in which it was generated ('pri' for primary analysis, 'round 1' and 'round 2' for advanced IMGT/V-QUEST-based analysis, without and with the indel option activated, respectively).
The advice section provides additional information for the reported issues and very often a link to comprehensive text below. The numbers in {} delineate the different advice and are for internal use, please ignore them for now.
hosted at the Bioinformatics Analysis Team / BAT