PathwayVoyager: pathway mapping using the Kyoto Encyclopedia of Genes and Genomes KEGG databaseReport as inadecuate




PathwayVoyager: pathway mapping using the Kyoto Encyclopedia of Genes and Genomes KEGG database - Download this document for free, or read online. Document in PDF available to download.

BMC Genomics

, 6:60

First Online: 03 May 2005Received: 21 December 2004Accepted: 03 May 2005

Abstract

BackgroundEqually important and challenging as genome annotation, is the subsequent classification of predicted genes into their respective pathways. The Kyoto Encyclopedia of Genes and Genomes KEGG represents a database consisting of known genes and their respective biochemical functionalities. Although accessible online, analyses of multiple genes are time consuming and are not suitable for analyzing data sets that are proprietary.

ResultsPresented here is a new software solution that utilizes the KEGG online database for pathway mapping of partial and whole prokaryotic genomes. PathwayVoyager retrieves user-defined subsets of the KEGG database and stores the data as local, blast-formatted databases. Previously selected datasets can be re-used, reducing run-time significantly. Whole or partial genomes can be automatically analyzed using NCBI-s BlastP algorithm and ORFs with similarities below the user-defined threshold will be marked on pathway maps. Multiple gene hits are sorted by similarity. Since no sequence information is transmitted over the Internet, PathwayVoyager is an ideal solution for pathway mapping and reconstruction of confidential DNA sequence data.

ConclusionPathwayVoyager represents an alternative approach to many already existing, more complex pathway reconstructions software solutions. This software does not require any dedicated hardware or software and is flexible and straightforward to use. It is ideally suited for environments where analyses on variable datasets are desired.

Electronic supplementary materialThe online version of this article doi:10.1186-1471-2164-6-60 contains supplementary material, which is available to authorized users.

Download fulltext PDF



Author: Eric Altermann - Todd R Klaenhammer

Source: https://link.springer.com/article/10.1186/1471-2164-6-60







Related documents