BACKGROUND: A large number of gene prediction programs for the human genome 
exist. These annotation tools use a variety of methods and data sources. In the 
recent ENCODE genome annotation assessment project (EGASP), some of the most 
commonly used and recently developed gene-prediction programs were 
systematically evaluated and compared on test data from the human genome. 
AUGUSTUS was among the tools that were tested in this project.
RESULTS: AUGUSTUS can be used as an ab initio program, that is, as a program 
that uses only one single genomic sequence as input information. In addition, it 
is able to combine information from the genomic sequence under study with 
external hints from various sources of information. For EGASP, we used genomic 
sequence alignments as well as alignments to expressed sequence tags (ESTs) and 
protein sequences as additional sources of information. Within the category of 
ab initio programs AUGUSTUS predicted significantly more genes correctly than 
any other ab initio program. At the same time it predicted the smallest number 
of false positive genes and the smallest number of false positive exons among 
all ab initio programs. The accuracy of AUGUSTUS could be further improved when 
additional extrinsic data, such as alignments to EST, protein and/or genomic 
sequences, was taken into account.
CONCLUSION: AUGUSTUS turned out to be the most accurate ab initio gene finder 
among the tested tools. Moreover it is very flexible because it can take 
information from several sources simultaneously into consideration.