SMART, a Simple Modular Architecture Research Tool - Development andApplications
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Zusammenfassung
In my thesis, I've used sequence data to analyse function and evolution of proteins and domains. Therefore, a system which reliably identifies domains and is able to correlate them with phylogenetic as well as co-occurence information was needed. I've developed SMART (a Simple Modular Architecture Research Tool), which allows the identification and annotation of genetically mobile domains and the analysis of domain architectures (http://smart.EMBL-Heidelberg.de). SMART is based on a relational database system which stores each domain found in a non-redundant protein database as well as search parameters and taxonomic information. The database is used to provide extensive annotation in respect to phyletic distribution, functional class, tertiary structures and cellular localisation. Today, SMART detects 500 domain families found in signalling, extracellular and chromatin associated proteins. Domain identification in SMART is based on high quality, hand curated alignments, which have been exploited in recent genomics studies. Comparisons of the domain distributions in eukaryotes and prokaryotes enabled distinctions to be made between the domains originating prior to the last common ancestor of all known life forms and those apparently originating as consequences of horizontal gene transfer events. A number of transfers of signalling domains from eukaryotes to bacteria were confidently identified, in contrast to only a single case of apparent transfer from eukaryotes to archaea. To estimate the size of human protein families involved in signalling proccesses, I developed a method which couples SMART with BLAST based searches to find possible novel genes in EST databases. Application of this method in a large scale analysis of 100 signalling domain families to a human EST database has led to the identification of ESTs representing more than 1000 novel human signalling genes.
Zusammenfassung in einer weiteren Sprache
In my thesis, I've used sequence data to analyse function and evolution of proteins and domains. Therefore, a system which reliably identifies domains and is able to correlate them with phylogenetic as well as co-occurence information was needed. I've developed SMART (a Simple Modular Architecture Research Tool), which allows the identification and annotation of genetically mobile domains and the analysis of domain architectures (http://smart.EMBL-Heidelberg.de). SMART is based on a relational database system which stores each domain found in a non-redundant protein database as well as search parameters and taxonomic information. The database is used to provide extensive annotation in respect to phyletic distribution, functional class, tertiary structures and cellular localisation. Today, SMART detects 500 domain families found in signalling, extracellular and chromatin associated proteins. Domain identification in SMART is based on high quality, hand curated alignments, which have been exploited in recent genomics studies. Comparisons of the domain distributions in eukaryotes and prokaryotes enabled distinctions to be made between the domains originating prior to the last common ancestor of all known life forms and those apparently originating as consequences of horizontal gene transfer events. A number of transfers of signalling domains from eukaryotes to bacteria were confidently identified, in contrast to only a single case of apparent transfer from eukaryotes to archaea. To estimate the size of human protein families involved in signalling proccesses, I developed a method which couples SMART with BLAST based searches to find possible novel genes in EST databases. Application of this method in a large scale analysis of 100 signalling domain families to a human EST database has led to the identification of ESTs representing more than 1000 novel human signalling genes.
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SCHULTZ, Jörg, 2001. SMART, a Simple Modular Architecture Research Tool - Development andApplications [Dissertation]. Konstanz: University of KonstanzBibTex
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