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TreeDomViewer: a tool for the visualization of phylogeny and protein domain structure

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      Abstract

      Phylogenetic analysis and examination of protein domains allow accurate genome annotation and are invaluable to study proteins and protein complex evolution. However, two sequences can be homologous without sharing statistically significant amino acid or nucleotide identity, presenting a challenging bioinformatics problem. We present TreeDomViewer, a visualization tool available as a web-based interface that combines phylogenetic tree description, multiple sequence alignment and InterProScan data of sequences and generates a phylogenetic tree projecting the corresponding protein domain information onto the multiple sequence alignment. Thereby it makes use of existing domain prediction tools such as InterProScan. TreeDomViewer adopts an evolutionary perspective on how domain structure of two or more sequences can be aligned and compared, to subsequently infer the function of an unknown homolog. This provides insight into the function assignment of, in terms of amino acid substitution, very divergent but yet closely related family members. Our tool produces an interactive scalar vector graphics image that provides orthological relationship and domain content of proteins of interest at one glance. In addition, PDF, JPEG or PNG formatted output is also provided. These features make TreeDomViewer a valuable addition to the annotation pipeline of unknown genes or gene products. TreeDomViewer is available at http://www.bioinformatics.nl/tools/treedom/.

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      Most cited references 19

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      The neighbor-joining method: a new method for reconstructing phylogenetic trees.

       N Saitou,  M Nei (1987)
      A new method called the neighbor-joining method is proposed for reconstructing phylogenetic trees from evolutionary distance data. The principle of this method is to find pairs of operational taxonomic units (OTUs [= neighbors]) that minimize the total branch length at each stage of clustering of OTUs starting with a starlike tree. The branch lengths as well as the topology of a parsimonious tree can quickly be obtained by using this method. Using computer simulation, we studied the efficiency of this method in obtaining the correct unrooted tree in comparison with that of five other tree-making methods: the unweighted pair group method of analysis, Farris's method, Sattath and Tversky's method, Li's method, and Tateno et al.'s modified Farris method. The new, neighbor-joining method and Sattath and Tversky's method are shown to be generally better than the other methods.
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        CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice.

        The sensitivity of the commonly used progressive multiple sequence alignment method has been greatly improved for the alignment of divergent protein sequences. Firstly, individual weights are assigned to each sequence in a partial alignment in order to down-weight near-duplicate sequences and up-weight the most divergent ones. Secondly, amino acid substitution matrices are varied at different alignment stages according to the divergence of the sequences to be aligned. Thirdly, residue-specific gap penalties and locally reduced gap penalties in hydrophilic regions encourage new gaps in potential loop regions rather than regular secondary structure. Fourthly, positions in early alignments where gaps have been opened receive locally reduced gap penalties to encourage the opening up of new gaps at these positions. These modifications are incorporated into a new program, CLUSTAL W which is freely available.
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          EMBOSS: the European Molecular Biology Open Software Suite.

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            Author and article information

            Affiliations
            1simpleLaboratory of Bioinformatics, Wageningen University and Research Centre PO Box 8128, 6700 ET Wageningen, The Netherlands
            2simpleCentre for BioSystems Genomics PO Box 98, 6700 AB Wageningen, The Netherlands
            3simpleKEYGENE NV PO Box 216 6700 AE Wageningen, The Netherlands
            Author notes
            *To whom correspondence should be addressed. Tel: +31 317 482 036; Fax: +31 317 483 584; Email: jack.leunissen@ 123456wur.nl
            Journal
            Nucleic Acids Res
            Nucleic Acids Research
            Nucleic Acids Research
            Oxford University Press
            0305-1048
            1362-4962
            01 July 2006
            01 July 2006
            14 July 2006
            : 34
            : Web Server issue
            : W104-W109
            1538806
            10.1093/nar/gkl171
            16844970
            © 2006 The Author(s)

            This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License ( http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commerical use, distribution, and reproduction in any medium, provided the original work is properly cited.

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            Genetics

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