Dataset Information

Integration of phenotypic metadata and protein similarity in Archaea using a spectral bipartitioning approach.

ABSTRACT: In order to simplify and meaningfully categorize large sets of protein sequence data, it is commonplace to cluster proteins based on the similarity of those sequences. However, it quickly becomes clear that the sequence flexibility allowed a given protein varies significantly among different protein families. The degree to which sequences are conserved not only differs for each protein family, but also is affected by the phylogenetic divergence of the source organisms. Clustering techniques that use similarity thresholds for protein families do not always allow for these variations and thus cannot be confidently used for applications such as automated annotation and phylogenetic profiling. In this work, we applied a spectral bipartitioning technique to all proteins from 53 archaeal genomes. Comparisons between different taxonomic levels allowed us to study the effects of phylogenetic distances on cluster structure. Likewise, by associating functional annotations and phenotypic metadata with each protein, we could compare our protein similarity clusters with both protein function and associated phenotype. Our clusters can be analyzed graphically and interactively online.

SUBMITTER: Hooper SD

PROVIDER: S-EPMC2673424 | biostudies-literature | 2009 Apr

REPOSITORIES: biostudies-literature

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Publications

Integration of phenotypic metadata and protein similarity in Archaea using a spectral bipartitioning approach.

Hooper Sean D SD Anderson Iain J IJ Pati Amrita A Dalevi Daniel D Mavromatis Konstantinos K Kyrpides Nikos C NC

Nucleic acids research 20090217 7

In order to simplify and meaningfully categorize large sets of protein sequence data, it is commonplace to cluster proteins based on the similarity of those sequences. However, it quickly becomes clear that the sequence flexibility allowed a given protein varies significantly among different protein families. The degree to which sequences are conserved not only differs for each protein family, but also is affected by the phylogenetic divergence of the source organisms. Clustering techniques that ...[more]

PMID: 19223325

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Project description:As increasingly more genomes are sequenced, the vast majority of proteins may only be annotated computationally, given experimental investigation is extremely costly. This highlights the need for computational methods to determine protein functions quickly and reliably. We believe dividing a protein family into subtypes which share specific functions uncommon to the whole family reduces the function annotation problem's complexity. Hence, this work's purpose is to detect isofunctional subfamilies inside a family of unknown function, while identifying differentiating residues. Similarity between protein pairs according to various properties is interpreted as functional similarity evidence. Data are integrated using genetic programming and provided to a spectral clustering algorithm, which creates clusters of similar proteins. The proposed framework was applied to well-known protein families and to a family of unknown function, then compared to ASMC. Results showed our fully automated technique obtained better clusters than ASMC for two families, besides equivalent results for other two, including one whose clusters were manually defined. Clusters produced by our framework showed great correspondence with the known subfamilies, besides being more contrasting than those produced by ASMC. Additionally, for the families whose specificity determining positions are known, such residues were among those our technique considered most important to differentiate a given group. When run with the crotonase and enolase SFLD superfamilies, the results showed great agreement with this gold-standard. Best results consistently involved multiple data types, thus confirming our hypothesis that similarities according to different knowledge domains may be used as functional similarity evidence. Our main contributions are the proposed strategy for selecting and integrating data types, along with the ability to work with noisy and incomplete data; domain knowledge usage for detecting subfamilies in a family with different specificities, thus reducing the complexity of the experimental function characterization problem; and the identification of residues responsible for specificity.

Project description:BACKGROUND: The chemical property and biological function of a protein is a direct consequence of its primary structure. Several algorithms have been developed which determine alignment and similarity of primary protein sequences. However, character based similarity cannot provide insight into the structural aspects of a protein. We present a method based on spectral similarity to compare subsequences of amino acids that behave similarly but are not aligned well by considering amino acids as mere characters. This approach finds a similarity score between sequences based on any given attribute, like hydrophobicity of amino acids, on the basis of spectral information after partial conversion to the frequency domain. RESULTS: Distance matrices of various branches of the human kinome, that is the full complement of human kinases, were developed that matched the phylogenetic tree of the human kinome establishing the efficacy of the global alignment of the algorithm. PKCd and PKCe kinases share close biological properties and structural similarities but do not give high scores with character based alignments. Detailed comparison established close similarities between subsequences that do not have any significant character identity. We compared their known 3D structures to establish that the algorithm is able to pick subsequences that are not considered similar by character based matching algorithms but share structural similarities. Similarly many subsequences with low character identity were picked between xyna-theau and xyna-clotm F/10 xylanases. Comparison of 3D structures of the subsequences confirmed the claim of similarity in structure. CONCLUSION: An algorithm is developed which is inspired by successful application of spectral similarity applied to music sequences. The method captures subsequences that do not align by traditional character based alignment tools but give rise to similar secondary and tertiary structures. The Spectral Similarity Score (SSS) is an extension to the conventional similarity methods and results indicate that it holds a strong potential for analysis of various biological sequences and structural variations in proteins.

Project description:Metadata plays an essential role in the long-term preservation, reuse, and interoperability of data. Nevertheless, creating useful metadata can be sufficiently difficult and weakly enough incentivized that many datasets may be accompanied by little or no metadata. One key challenge is, therefore, how to make metadata creation easier and more valuable. We present a solution that involves creating domain-specific metadata schemes that are as complex as necessary and as simple as possible. These goals are achieved by co-development between a metadata expert and the researchers (i.e., the data creators). The final product is a bespoke metadata scheme into which researchers can enter information (and validate it) via the simplest of interfaces: a web browser application and a spreadsheet.We provide the R package dmdScheme (dmdScheme: An R package for working with domain specific MetaData schemes (Version v0.9.22), 2019) for creating a template domain-specific scheme. We describe how to create a domain-specific scheme from this template, including the iterative co-development process, and the simple methods for using the scheme, and simple methods for quality assessment, improvement, and validation.The process of developing a metadata scheme following the outlined approach was successful, resulting in a metadata scheme which is used for the data generated in our research group. The validation quickly identifies forgotten metadata, as well as inconsistent metadata, therefore improving the quality of the metadata. Multiple output formats are available, including XML.Making the provision of metadata easier while also ensuring high quality must be a priority for data curation initiatives. We show how both objectives are achieved by close collaboration between metadata experts and researchers to create domain-specific schemes. A near-future priority is to provide methods to interface domain-specific schemes with general metadata schemes, such as the Ecological Metadata Language, to increase interoperability.

Dataset Information

Integration of phenotypic metadata and protein similarity in Archaea using a spectral bipartitioning approach.

Publications

Integration of phenotypic metadata and protein similarity in Archaea using a spectral bipartitioning approach.

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