+ Site Statistics
References:
52,654,530
Abstracts:
29,560,856
PMIDs:
28,072,755
+ Search Articles
+ Subscribe to Site Feeds
Most Shared
PDF Full Text
+ PDF Full Text
Request PDF Full Text
+ Follow Us
Follow on Facebook
Follow on Twitter
Follow on LinkedIn

+ Translate
+ Recently Requested

Automated system for gene annotation and metabolic pathway reconstruction using general sequence databases



Automated system for gene annotation and metabolic pathway reconstruction using general sequence databases



Chemistry and Biodiversity 4(11): 2593-2602



Despite the growing number of genomes published or currently being sequenced, there is a relative paucity of software for functional classification of newly discovered genes and their assignment to metabolic pathways. Available software for such analyses has a very steep learning curve and requires the installation, configuration, and maintenance of large amounts of complex infrastructure, including complementary software and databases. Many such tools are restricted to one or a few data sources and classification schemes. In this work, we report an automated system for gene annotation and metabolic pathway reconstruction (ASGARD), which was designed to be powerful and generalizable, yet simple for the biologist to install and run on centralized, commonly available computers. It avoids the requirement for complex resources such as relational databases and web servers, as well as the need for administrator access to the operating system. Our methodology contributes to a more rapid investigation of the potential biochemical capabilities of genes and genomes by the biological researcher, and is useful in biochemical as well as comparative and evolutionary studies of pathways and networks.

(PDF emailed within 0-6 h: $19.90)

Accession: 051727057

Download citation: RISBibTeXText

PMID: 18027373

DOI: 10.1002/cbdv.200790212


Related references

Using metabolic pathway databases for functional annotation. Trends in Genetics 14(8): 332-333, 1998

Updating annotations with the distributed annotation system and the automated sequence annotation pipeline. Bioinformatics 28(21): 2858-2859, 2013

Automated DNA chip annotation tables at IFOM: the importance of synchronisation and cross-referencing of sequence databases. Applied Bioinformatics 2(4): 245-249, 2004

An automated system for sequence analysis, annotation, and comparison. American Journal of Human Genetics 67(4 Supplement 2): 257, October, 2000

Automated Gene Ontology annotation for anonymous sequence data. Nucleic Acids Research 31(13): 3712-3715, 2003

RiceGAAS: an automated annotation system and database for rice genome sequence. Nucleic Acids Research 30(1): 98-102, 2001

HoSeqI: automated homologous sequence identification in gene family databases. Bioinformatics 22(14): 1786-1787, 2006

Tidying up international nucleotide sequence databases: ecological, geographical and sequence quality annotation of its sequences of mycorrhizal fungi. Plos One 6(9): E24940, 2012

GOblet: annotation of anonymous sequence data with gene ontology and pathway terms. Journal of Integrative Bioinformatics 5(2), 2010

Tunable machine vision-based strategy for automated annotation of chemical databases. Journal of Chemical Information and Modeling 49(8): 1993-2001, 2009

Development and evaluation of an automated annotation pipeline and cDNA annotation system. Genome Research 13(6b): 1542-1551, 2003

The annotation-enriched non-redundant patent sequence databases. Database 2013: Bat005, 2013

Automatic genome annotation and the status of sequence databases. Bioinformatics and genomes: current perspectives: 107-121, 2003

GeneLook: a novel ab initio gene identification system suitable for automated annotation of prokaryotic sequences. Gene 346: 115-125, 2005

Editorial board-authored annotation drivers for sequence databases. FASEB Journal 12(8): A1396, April 24, 1998