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      CABRA: Cluster and Annotate Blast Results Algorithm

      brief-report
      Author(s): ,
      Publication date (Electronic):
      Journal: BMC Research Notes
      Publisher: BioMed Central
      Keywords: Clustering, BLAST search, Web tool, Computational biology

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          Abstract

          Background

          Basic local alignment search tool (BLAST) searches are frequently used to look for homologous sequences and to annotate a query protein, but the increasing size of protein databases makes it difficult to review all results from a similarity search.

          Findings

          We developed a web tool called Cluster and Annotate Blast Results Algorithm (CABRA), which enables a rapid BLAST search in a variety of updated reference proteomes, and provides a new way to functionally evaluate the results by the subsequent clustering of the hits and annotation of the clusters. The tool can be accessed from the following web-resource: http://cbdm-01.zdv.uni-mainz.de/~munoz/CABRA.

          Conclusions

          Cluster and Annotate Blast Results Algorithm simplifies the analysis of the results of a BLAST search by providing an overview of the result’s annotations organized in clusters that can be iteratively modified by the user.

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          Most cited references7

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          The Fpg/Nei family of DNA glycosylases: substrates, structures, and search for damage.

          Aishwarya Prakash, Sylvie Doublié, Susan S Wallace (2012)
          During the initial stages of the base excision DNA repair pathway, DNA glycosylases are responsible for locating and removing the majority of endogenous oxidative base lesions. The bifunctional formamidopyrimidine DNA glycosylase (Fpg) and endonuclease VIII (Nei) are members of the Fpg/Nei family, one of the two families of glycosylases that recognize oxidized DNA bases, the other being the HhH/GPD (or Nth) superfamily. Structural and biochemical developments over the past decades have led to novel insights into the mechanism of damage recognition by the Fpg/Nei family of enzymes. Despite the overall structural similarity among members of this family, these enzymes exhibit distinct features that make them unique. This review summarizes the current structural knowledge of the Fpg/Nei family members, emphasizes their substrate specificities, and describes how these enzymes search for lesions. Copyright © 2012 Elsevier Inc. All rights reserved.
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            FastaHerder2: Four Ways to Research Protein Function and Evolution with Clustering and Clustered Databases.

            Pablo Mier, Miguel Andrade-Navarro (2016)
            The accelerated growth of protein databases offers great possibilities for the study of protein function using sequence similarity and conservation. However, the huge number of sequences deposited in these databases requires new ways of analyzing and organizing the data. It is necessary to group the many very similar sequences, creating clusters with automated derived annotations useful to understand their function, evolution, and level of experimental evidence. We developed an algorithm called FastaHerder2, which can cluster any protein database, putting together very similar protein sequences based on near-full-length similarity and/or high threshold of sequence identity. We compressed 50 reference proteomes, along with the SwissProt database, which we could compress by 74.7%. The clustering algorithm was benchmarked using OrthoBench and compared with FASTA HERDER, a previous version of the algorithm, showing that FastaHerder2 can cluster a set of proteins yielding a high compression, with a lower error rate than its predecessor. We illustrate the use of FastaHerder2 to detect biologically relevant functional features in protein families. With our approach we seek to promote a modern view and usage of the protein sequence databases more appropriate to the postgenomic era.
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              Identification of a zinc finger domain in the human NEIL2 (Nei-like-2) protein.

              Aditi Das, Lavanya Rajagopalan, Venkatarajan S Mathura … (2004)
              The recently identified human NEIL2 (Nei-like-2) protein, a DNA glycosylase/AP lyase specific for oxidatively damaged bases, shares structural features and reaction mechanism with the Escherichia coli DNA glycosylases, Nei and Fpg. Amino acid sequence analysis of NEIL2 suggested it to have a zinc finger-like Nei/Fpg. However, the Cys-X2-His-X16-Cys-X2-Cys (CHCC) motif present near the C terminus of NEIL2 is distinct from the zinc finger motifs of Nei/Fpg, which are of the C4 type. Here we show the presence of an equimolar amount of zinc in NEIL2 by inductively coupled plasma mass spectrometry. Individual mutations of Cys-291, His-295, Cys-315, and Cys-318, candidate residues for coordinating zinc, inactivated the enzyme by abolishing its DNA binding activity. H295A and C318S mutants were also shown to lack bound zinc, and a significant change in their secondary structure was revealed by CD spectra analysis. Molecular modeling revealed Arg-310 of NEIL2 to be a critical residue in its zinc binding pocket, which is highly conserved throughout the Fpg/Nei family. A R310Q mutation significantly reduced the activity of NEIL2. We thereby conclude that the zinc finger motif in NEIL2 is essential for its structural integrity and enzyme activity.
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                Author and article information

                Contributors
                Pablo Mier: munoz@uni-mainz.com
                Miguel A. Andrade-Navarro: andrade@uni-mainz.de
                Journal
                Journal ID (nlm-ta): BMC Res Notes
                Journal ID (iso-abbrev): BMC Res Notes
                Title: BMC Research Notes
                Publisher: BioMed Central (London )
                ISSN (Electronic): 1756-0500
                Publication date (Electronic): 30 April 2016
                Publication date PMC-release: 30 April 2016
                Publication date Collection: 2016
                Volume: 9
                Electronic Location Identifier: 253
                Affiliations
                [ ]Faculty of Biology, JGU Mainz, Gresemundweg, 2, 55128 Mainz, Germany
                [ ]Institute of Molecular Biology, Ackermannweg 4, 55128 Mainz, Germany
                Article
                Publisher ID: 2062
                DOI: 10.1186/s13104-016-2062-y
                PMC ID: 4851773
                PubMed ID: 27129717
                SO-VID: 353c68bd-8a92-4013-81e9-0bbfbc47dd03
                Copyright © © Mier and Andrade-Navarro. 2016
                License:

                Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License ( http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver ( http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

                History
                Date received : 20 April 2016
                Date accepted : 25 April 2016
                Categories
                Subject: Technical Note
                Custom metadata
                issue-copyright-statement © The Author(s) 2016

                ScienceOpen disciplines: Medicine
                Keywords: clustering,blast search,web tool,computational biology
                Data availability:
                ScienceOpen disciplines: Medicine
                Keywords: clustering, blast search, web tool, computational biology

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