Dataset Information

SCALOP: sequence-based antibody canonical loop structure annotation.

ABSTRACT:

Motivation

Canonical forms of the antibody complementarity-determining regions (CDRs) were first described in 1987 and have been redefined on multiple occasions since. The canonical forms are often used to approximate the antibody binding site shape as they can be predicted from sequence. A rapid predictor would facilitate the annotation of CDR structures in the large amounts of repertoire data now becoming available from next generation sequencing experiments.

Results

SCALOP annotates CDR canonical forms for antibody sequences, supported by an auto-updating database to capture the latest cluster information. Its accuracy is comparable to that of a standard structural predictor but it is 800 times faster. The auto-updating nature of SCALOP ensures that it always attains the best possible coverage.

Availability and implementation

SCALOP is available as a web application and for download under a GPLv3 license at opig.stats.ox.ac.uk/webapps/scalop.

Supplementary information

Supplementary data are available at Bioinformatics online.

SUBMITTER: Wong WK

PROVIDER: S-EPMC6513161 | biostudies-literature | 2019 May

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

SCALOP: sequence-based antibody canonical loop structure annotation.

Wong Wing Ki WK Georges Guy G Ros Francesca F Kelm Sebastian S Lewis Alan P AP Taddese Bruck B Leem Jinwoo J Deane Charlotte M CM

Bioinformatics (Oxford, England) 20190501 10

<h4>Motivation</h4>Canonical forms of the antibody complementarity-determining regions (CDRs) were first described in 1987 and have been redefined on multiple occasions since. The canonical forms are often used to approximate the antibody binding site shape as they can be predicted from sequence. A rapid predictor would facilitate the annotation of CDR structures in the large amounts of repertoire data now becoming available from next generation sequencing experiments.<h4>Results</h4>SCALOP anno ...[more]

PMID: 30321295

Similar Datasets

Project description:BackgroundMicrosporidia are a large taxon of intracellular pathogens characterized by extraordinarily streamlined genomes with unusually high sequence divergence and many species-specific adaptations. These unique factors pose challenges for traditional genome annotation methods based on sequence similarity. As a result, many of the microsporidian genomes sequenced to date contain numerous genes of unknown function. Recent innovations in rapid and accurate structure prediction and comparison, together with the growing amount of data in structural databases, provide new opportunities to assist in the functional annotation of newly sequenced genomes.ResultsIn this study, we established a workflow that combines sequence and structure-based functional gene annotation approaches employing a ChimeraX plugin named ANNOTEX (Annotation Extension for ChimeraX), allowing for visual inspection and manual curation. We employed this workflow on a high-quality telomere-to-telomere sequenced tetraploid genome of Vairimorpha necatrix. First, the 3080 predicted protein-coding DNA sequences, of which 89% were confirmed with RNA sequencing data, were used as input. Next, ColabFold was used to create protein structure predictions, followed by a Foldseek search for structural matching to the PDB and AlphaFold databases. The subsequent manual curation, using sequence and structure-based hits, increased the accuracy and quality of the functional genome annotation compared to results using only traditional annotation tools. Our workflow resulted in a comprehensive description of the V. necatrix genome, along with a structural summary of the most prevalent protein groups, such as the ricin B lectin family. In addition, and to test our tool, we identified the functions of several previously uncharacterized Encephalitozoon cuniculi genes.ConclusionWe provide a new functional annotation tool for divergent organisms and employ it on a newly sequenced, high-quality microsporidian genome to shed light on this uncharacterized intracellular pathogen of Lepidoptera. The addition of a structure-based annotation approach can serve as a valuable template for studying other microsporidian or similarly divergent species.

Dataset Information

SCALOP: sequence-based antibody canonical loop structure annotation.

Motivation

Results

Availability and implementation

Supplementary information

Publications

SCALOP: sequence-based antibody canonical loop structure annotation.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets