PubMed · 15628097
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Elizabeth Hetzler, Alan Turner. Analysis experiences using information visualization.. https://doi.org/10.1109/mcg.2004.22
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BACKGROUND: A large volume of data and information about genes and gene products has been stored in various molecular biology databases. A major challenge for knowledge discovery using these databases is to identify related genes and gene products in disparate databases. The development of Gene Ontology (GO) as a common vocabulary for annotation allows integrated queries across multiple databases and identification of semantically related genes and gene products (i.e., genes and gene products that have similar GO annotations). Meanwhile, dozens of tools have been developed for browsing, mining or editing GO terms, their hierarchical relationships, or their "associated" genes and gene products (i.e., genes and gene products annotated with GO terms). Tools that allow users to directly search and inspect relations among all GO terms and their associated genes and gene products from multiple databases are needed. RESULTS: We present a standalone package called DynGO, which provides several advanced functionalities in addition to the standard browsing capability of the official GO browsing tool (AmiGO). DynGO allows users to conduct batch retrieval of GO annotations for a list of genes and gene products, and semantic retrieval of genes and gene products sharing similar GO annotations. The result are shown in an association tree organized according to GO hierarchies and supported with many dynamic display options such as sorting tree nodes or changing orientation of the tree. For GO curators and frequent GO users, DynGO provides fast and convenient access to GO annotation data. DynGO is generally applicable to any data set where the records are annotated with GO terms, as illustrated by two examples. CONCLUSION: We have presented a standalone package DynGO that provides functionalities to search and browse GO and its association databases as well as several additional functions such as batch retrieval and semantic retrieval. The complete documentation and software are freely available for download from the website http://biocreative.ifsm.umbc.edu/dyngo.
The Fragnostic (http://ffas.burnham.org/Fragnostic) web tool implements a novel and useful view of protein structure space. We mined a non-redundant subset of the PDB for common fragments shared between proteins inhabiting different SCOP folds. Subsequently, we formulated an inter-fold similarity measure based on fragment sharing. Fold space is described as a graph whose nodes are folds between which the edges are drawn depending on the extent of fragment sharing. In this fashion, Fragnostic helps discover meaningful relationships between proteins belonging to different folds, based on sharing similar fragments in the proteins comprising those folds. Distant fold similarity information is supplemented by annotations taken from Gene Ontology, SCOP and CATH. Overall, Fragnostic is a tool which helps discover structural and functional relationships between proteins which are distantly related or seemingly unrelated.
Comparative analysis of genomic sequences is a powerful approach to discover functional sites in these sequences. Herein, we present a WWW-based software system for multiple alignment of genomic sequences. We use the local alignment tool CHAOS to rapidly identify chains of pairwise similarities. These similarities are used as anchor points to speed up the DIALIGN multiple-alignment program. Finally, the visualization tool ABC is used for interactive graphical representation of the resulting multiple alignments. Our software is available at Göttingen Bioinformatics Compute Server (GOBICS) at http://dialign.gobics.de/chaos-dialign-submission.