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Paratome: an online tool for systematic identification of antigen-binding regions in antibodies based on sequence or structure.

ABSTRACT: Antibodies are capable of specifically recognizing and binding antigens. Identification of the antigen-binding site, commonly dubbed paratope, is of high importance both for medical and biological applications. To date, the identification of antigen-binding regions (ABRs) relies on tools for the identification of complementarity-determining regions (CDRs). However, we have shown that up to 22% of the residues that actually bind the antigen fall outside the traditionally defined CDRs. The Paratome web server predicts the ABRs of an antibody, given its amino acid sequence or 3D structure. It is based on a set of consensus regions derived from a structural alignment of a non-redundant set of all known antibody-antigen complexes. Given a query sequence or structure, the server identifies the regions in the query antibody that correspond to the consensus ABRs. An independent set of antibody-antigen complexes was used to test the server and it was shown to correctly identify at least 94% of the antigen-binding residues. The Paratome web server is freely available at http://www.ofranlab.org/paratome/.

SUBMITTER: Kunik V

PROVIDER: S-EPMC3394289 | biostudies-literature | 2012 Jul

REPOSITORIES: biostudies-literature

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Paratome: an online tool for systematic identification of antigen-binding regions in antibodies based on sequence or structure.

Kunik Vered V Ashkenazi Shaul S Ofran Yanay Y

Nucleic acids research 20120606 Web Server issue

Antibodies are capable of specifically recognizing and binding antigens. Identification of the antigen-binding site, commonly dubbed paratope, is of high importance both for medical and biological applications. To date, the identification of antigen-binding regions (ABRs) relies on tools for the identification of complementarity-determining regions (CDRs). However, we have shown that up to 22% of the residues that actually bind the antigen fall outside the traditionally defined CDRs. The Paratom ...[more]

PMID: 22675071

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Project description:Novel sequences are DNA sequences present in an individual's genome but absent in the human reference assembly. They are predicted to be biologically important, both individual and population specific, and consistent with the known human migration paths. Recent works have shown that an average person harbors 2-5 Mb of such sequences and estimated that the human pan-genome contains as high as 19-40 Mb of novel sequences. To identify them in a de novo genome assembly, some existing sequence aligners have been used but no computational method has been specifically proposed for this task. In this work, we developed NSIT (Novel Sequence Identification Tool), a software that can accurately and efficiently identify novel sequences in an individual's de novo whole genome assembly. We identified and characterized 1.1 Mb, 1.2 Mb, and 1.0 Mb of novel sequences in NA18507 (African), YH (Asian), and NA12878 (European) de novo genome assemblies, respectively. Our results show very high concordance with the previous work using the respective reference assembly. In addition, our results using the latest human reference assembly suggest that the amount of novel sequences per individual may not be as high as previously reported. We additionally developed a graphical viewer for comparisons of novel sequence contents. The viewer also helped in identifying sequence contamination; we found 130 kb of Epstein-Barr virus sequence in the previously published NA18507 novel sequences as well as 287 kb of zebrafish repeats in NA12878 de novo assembly. NSIT requires [Formula: see text]2GB of RAM and 1.5-2 hrs on a commodity desktop. The program is applicable to input assemblies with varying contig/scaffold sizes, ranging from 100 bp to as high as 50 Mb. It works in both 32-bit and 64-bit systems and outperforms, by large margins, other fast sequence aligners previously applied to this task. To our knowledge, NSIT is the first software designed specifically for novel sequence identification in a de novo human genome assembly.

Dataset Information

Paratome: an online tool for systematic identification of antigen-binding regions in antibodies based on sequence or structure.

Publications

Paratome: an online tool for systematic identification of antigen-binding regions in antibodies based on sequence or structure.

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