Bioinformatics publications

We seek to determine the accuracy of computational methods for predicting metabolic pathways in sequenced genomes, and to understand the contributions of both the prediction algorithms, and the reference pathway…

We define the process of annotating a previously annotated genome sequence as 're-annotation', and examine the strengths and weaknesses of current manual and automatic genome-wide re-annotation approaches.

The Pathway Tools is a reusable, production-quality software environment for creating a type of MOD called a Pathway/Genome Database (PGDB).

MetaCyc is a metabolic-pathway database that describes 445 pathways and 1115 enzymes occurring in 158 organisms.

The 5.67-megabase genome of the plant pathogen Agrobacterium tumefaciens C58 consists of a circular chromosome, a linear chromosome, and two plasmids.

We present an algorithm that solves two related problems in the analysis of metabolic networks stored within a pathway/genome database.

This document describes a language called XOL, is designed to provide a format for exchanging ontology definitions among a set of interested parties.

Here we present a computational analysis of the global properties of that network, which consists of 744 reactions that are catalyzed by 607 enzymes.

The article explores the notion of computing with function, and explains the importance of ontologies of function to bioinformatics.

Both databases are queried using the Pathway Tools graphical user interface, which provides a wide variety of query operations and visualization tools.

This paper reports on an effort among the authors to evaluate alternative ontology-exchange languages, and to recommend one or more languages for use within the larger bioinformatics community.