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PAVE EST Data Description

PAVE EST Data Description

Rice EST libraries were produced by Guo-liang Wang at Ohio State University and sequenced by the Arizona Genomics Institute. Magnaporthe EST libraries were produced by Daniel Ebbole at Texas A&M University.

Analysis [ Top ]
PAVE version 0.2 (Program for Assembling and Viewing ESTs), developed at AGCoL and partially supported by the MGOS project, is used for the EST assemblies. Forward and reverse pairs of ESTs are first checked for significant overlap. If such an overlap is found, the "mate pairs" are regarded as a single EST throughout the assembly process, being pulled back apart at the end. PAcE[1] is used for the initial clustering. Cap3[2] is run on each cluster to generate initial contigs. These contigs are then split into "correct" contigs as based on mate pair information and optional genomic BLAT[3] alignments and UniProt[4] BLASTX[5] alignments, then "self-blasted" using BLASTN[5] and merged together based on these results. Clusters are determined by first regarding each contig as a cluster, then merging two clusters if they each contain a mate from a single clone. This is continued until no more merges are possible.

The rice cDNAs[6] are included to aid in the assembly of the ESTs. Every contig displayed in PAVE has at least one EST.

The Published Rice Assembly was built using PAVE version 0.1, and was used for the analysis in [7].

The Published Magnaporthe Assembly was built as described in [8].


References [ Top ]
[1] Kalyanaraman, A., Aluru, S., Kothari, S. & Brendel, V. (2003). Efficient clustering of large EST data sets on parallel computers. Nucl. Acids Res. 31, 2963-2974.

[2] Huang, X., and Madan, A. (1999). CAP3: A DNA sequence assembly program. Genome Res 9, 868-87 7. Website

[3] Kent, W.J. (2002). BLAT--the BLAST-like alignment tool. Genome Res 12, 656-66

[4] Boeckmann, B., Bairoch, A., Apweiler, R., Blatter, M.C., Estreicher, A., Gasteiger, E., Martin, M.J., Michoud, K., O'Donovan, C., Phan, I., Pilbout, S., and Schneider, M. (2003). The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Res 31, 365-370.

[5] Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang, J., Zhang, Z., Miller, W., and Lipman, D.J. (1997). Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25, 3389-3402

[6] The Rice Full Length cDNA Consortium (2003) . Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice. Science 301, 376-379.

[7] Chatchawan Jantasuriyarat, Malali Gowda, Karl Haller, Jamie Hatfield, Guodong Lu, Eric Stahlberg, Bo Zhou, Huameng Li, HyRan Kim, Yeisoo Yu, Ralph A. Dean, Rod A. Wing, Carol Soderlund, and Guo-Liang Wang (2005). Large-Scale Identification of Expressed Sequence Tags Involved in Rice and Rice Blast Fungus Interaction. Plant Physiology 138, 105-115.

[8] Daniel J. Ebbole, Yuan Jin, Micheal Thon, Huaqin Pan, Eric Bhattari, Terry Thomas, and Ralph Dean (2004). Gene Discovery and Gene Expression in the Rice Blast Fungus, Magnaporthe grisea: Analysis of Expressed Sequence Tags. MPMI 17, 1337-1347. This work was funded in part by USDA-IFAFS #00-52100-9682. PDF