A strategy for assembling the maize (Zea mays L.) genome.
Because the bulk of the maize (Zea mays L.) genome consists of repetitive sequences, sequencing efforts are being targeted to its 'gene-rich' fraction. Traditional assembly programs are inadequate for this approach because they are optimized for a uniform sampling of the genome and inherently lack the ability to differentiate highly similar paralogs.


RESULTS
We report the development of bioinformatics tools for the accurate assembly of the maize genome. This software, which is based on innovative parallel algorithms to ensure scalability, assembled 730,974 genomic survey sequences fragments in 4 h using 64 Pentium III 1.26 GHz processors of a commodity cluster. Algorithmic innovations are used to reduce the number of pairwise alignments significantly without sacrificing quality. Clone pair information was used to estimate the error rate for improved differentiation of polymorphisms versus sequencing errors. The assembly was also used to evaluate the effectiveness of various filtering strategies and thereby provide information that can be used to focus subsequent sequencing efforts.
Emrich
Scott J
SJ
Bioinformatics and Computational Biology Graduate Program, Iowa State University, Ames, IA 50011, USA.
Aluru
Srinivas
S
Fu
Yan
Y
Wen
Tsui-Jung
TJ
Narayanan
Mahesh
M
Guo
Ling
L
Ashlock
Daniel A
DA
Schnable
Patrick S
PS
D000465:Algorithms; D003205:Computing Methodologies; D003628:Database Management Systems; D030561:Databases, Nucleic Acid; D020869:Gene Expression Profiling / Q000379:methods*; D018745:Genome, Plant; D012091:Repetitive Sequences, Nucleic Acid / Q000235:genetics*; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software; D012985:Software Design; D003313:Zea mays / Q000235:genetics*