A database of immunoglobulins with integrated tools: DIGIT

Chailyan, Anna; Tramontano, Anna; Marcatili, Paolo

doi:10.1093/nar/gkr806

Cited by 36 publications

(41 citation statements)

References 20 publications

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“…All non-ribosomal reads were mapped to a library containing the Bos taurus germline V, D and J genes [19, 20] (courtesy of authors Antti Livanainen and Ulrike S. Diesterbeck), and mature antibody sequences were retrieved from the DIGIT database [21] using TopHat2 software with relaxed parameters allowing for up to 30 mismatches, 50 gaps, and both should sum up to an overall edit distance of no more than 60. This was done to take into account somatic mutations and possible missing germ lines in the currently sequenced bovine antibody gene repertoire.…”

Section: Methodsmentioning

confidence: 99%

A novel approach to probe host-pathogen interactions of bovine digital dermatitis, a model of a complex polymicrobial infection

et al. 2016

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BackgroundPolymicrobial infections represent a great challenge for the clarification of disease etiology and the development of comprehensive diagnostic or therapeutic tools, particularly for fastidious and difficult-to-cultivate bacteria. Using bovine digital dermatitis (DD) as a disease model, we introduce a novel strategy to study the pathogenesis of complex infections.ResultsThe strategy combines meta-transcriptomics with high-density peptide-microarray technology to screen for in vivo-expressed microbial genes and the host antibody response at the site of infection. Bacterial expression patterns supported the assumption that treponemes were the major DD pathogens but also indicated the active involvement of other phyla (primarily Bacteroidetes). Bacterial genes involved in chemotaxis, flagellar synthesis and protection against oxidative and acidic stress were among the major factors defining the disease.ConclusionsThe extraordinary diversity observed in bacterial expression, antigens and host antibody responses between individual cows pointed toward microbial variability as a hallmark of DD. Persistence of infection and DD reinfection in the same individual is common; thus, high microbial diversity may undermine the host’s capacity to mount an efficient immune response and maintain immunological memory towards DD. The common antigenic markers identified here using a high-density peptide microarray address this issue and may be useful for future preventive measures against DD.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3341-7) contains supplementary material, which is available to authorized users.

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Section: Methodsmentioning

confidence: 99%

A novel approach to probe host-pathogen interactions of bovine digital dermatitis, a model of a complex polymicrobial infection

et al. 2016

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“…We built a ''test'' data set by querying the DIGIT database (29) for all available human Igs for which the paired sequences of the L and H chains were available. After inspecting the Ig description contained in the DIGIT database and the related PubMed entry, we discarded all Igs for which no reference to any published article could be found or not corresponding to an entry in Entrez Nucleotide (http://www.ncbi.nlm.nih.gov/nuccore/), as well as all Igs already contained in our initial CLL data set.…”

Section: Ig Data Setsmentioning

confidence: 99%

“…After inspecting the Ig description contained in the DIGIT database and the related PubMed entry, we discarded all Igs for which no reference to any published article could be found or not corresponding to an entry in Entrez Nucleotide (http://www.ncbi.nlm.nih.gov/nuccore/), as well as all Igs already contained in our initial CLL data set. We ended up with 2441 Igs for which complete information on canonical structures, loop length, and mutation rates could be retrieved using the tools provided by DIGIT (29).…”

Section: Ig Data Setsmentioning

confidence: 99%

Igs Expressed by Chronic Lymphocytic Leukemia B Cells Show Limited Binding-Site Structure Variability

Marcatili

Ghiotto

Tenca

et al. 2013

The Journal of Immunology

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Ag selection has been suggested to play a role in chronic lymphocytic leukemia (CLL) pathogenesis, but no large-scale analysis has been performed so far on the structure of the Ag-binding sites (ABSs) of leukemic cell Igs. We sequenced both H and L chain V(D)J rearrangements from 366 CLL patients and modeled their three-dimensional structures. The resulting ABS structures were clustered into a small number of discrete sets, each containing ABSs with similar shapes and physicochemical properties. This structural classification correlates well with other known prognostic factors such as Ig mutation status and recurrent (stereotyped) receptors, but it shows a better prognostic value, at least in the case of one structural cluster for which clinical data were available. These findings suggest, for the first time, to our knowledge, on the basis of a structural analysis of the Ab-binding sites, that selection by a finite quota of antigenic structures operates on most CLL cases, whether mutated or unmutated

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“…Tabhu, a set of tools to aid with antibody humanization [41] (circe.med.uniroma1.it/tabhu/) and Digit [42], a database of antibody variable domain sequences (circe.med.uniroma1.it/digit/).…”

mentioning

confidence: 99%

abYsis: Integrated Antibody Sequence and Structure—Management, Analysis, and Prediction

Swindells¹,

Porter

Couch

et al. 2017

Journal of Molecular Biology

145

134

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abYsis is a web-based antibody research system that includes an integrated database of antibody sequence and structure data. The system can be interrogated in numerous ways -from simple text and sequence searches to sophisticated queries that apply 3D structural constraints. The publicly available version includes pre-analysed sequence data from EMBL-ENA and Kabat as well as structure data from the PDB. A researcher's own sequences can also be analysed through the web interface.A defining characteristic of abYsis is that sequences are automatically numbered with a series of popular schemes such as Kabat and Chothia and then annotated with key information such as CDRs and potential post-translational modifications. A unique aspect of abYsis is a set of residue frequency tables for each position in an antibody, allowing 'unusual residues' (those rarely seen at a particular position) to be highlighted and decisions to be made on which mutations may be acceptable. This is especially useful when comparing antibodies from different species.

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A database of immunoglobulins with integrated tools: DIGIT

Cited by 36 publications

References 20 publications

A novel approach to probe host-pathogen interactions of bovine digital dermatitis, a model of a complex polymicrobial infection

A novel approach to probe host-pathogen interactions of bovine digital dermatitis, a model of a complex polymicrobial infection

Igs Expressed by Chronic Lymphocytic Leukemia B Cells Show Limited Binding-Site Structure Variability

abYsis: Integrated Antibody Sequence and Structure—Management, Analysis, and Prediction

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