Bioinformatics Vol. 17 no. 1 2001
Pages 44-57
© 2001 Oxford University Press
Original Paper |
Functional and structural genomics using PEDANT
1 GSF-Forschungszentrum
für Umwelt und Gesundheit, Munich
Information Center for Protein Sequences (MIPS) am
Max-Planck-Institut für Biochemie, Am
Klopferspitz 18, 82152 Martinsried, Germany
2 Biomax Informatics AG, Lochhamer
Straße 11, 82152 Martinsried, Germany
Received on April 28, 2000
; revised on June 23, 2000
; accepted on June 23, 2000
Motivation: Enormous demand for fast and accurate analysis of biological sequences is fuelled by the pace of genome analysis efforts. There is also an acute need in reliable up-to-date genomic databases integrating both functional and structural information. Here we describe the current status of the PEDANT software system for high-throughput analysis of large biological sequence sets and the genome analysis server associated with it.
Results: The principal features of PEDANT are: (i) completely automatic processing of data using a wide range of bioinformatics methods, (ii) manual refinement of annotation, (iii) automatic and manual assignment of gene products to a number of functional and structural categories, (iv) extensive hyperlinked protein reports, and (v) advanced DNA and protein viewers. The system is easily extensible and allows to include custom methods, databases, and categories with minimal or no programming effort. PEDANT is actively used as a collaborative environment to support several on-going genome sequencing projects. The main purpose of the PEDANT genome database is to quickly disseminate well-organized information on completely sequenced and unfinished genomes. It currently includes 80 genomic sequences and in many cases serves as the only source of exhaustive information on a given genome. The database also acts as a vehicle for a number of research projects in bioinformatics. Using SQL queries, it is possible to correlate a large variety of pre-computed properties of gene products encoded in complete genomes with each other and compare them with data sets of special scientific interest. In particular, the availability of structural predictions for over 300 000 genomic proteins makes PEDANT the most extensive structural genomics resource available on the web.
Availability: The PEDANT genome analysis server is available at http://pedant.mips.biochem.mpg.de.
Contact: Genome sequencing centres interested in inclusion of their sequences in the PEDANT database should contact Dmitrij Frishman (frishman{at}mips.biochem.mpg.de).
* To whom correspondence should be addressed.
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