PlantTribes - ESTstat: Web-based software for statistical analysis of EST library samples

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ESTstat v 1.0 implements the statistical algorithms of Wang et al. 2004a, Wang and Lindsay (2004) to provide an automated solution to quantitative analysis of EST data. The current version of ESTstat uses CAP3 clustering results including .ace and .singlets files as input to realize the following functions:

1. Summarize the CAP3 clustering result into gene cluster profile data defined as n=(n1, n2, ... ) where ni stands for the number of genes with i ESTs
2. For 5' ESTs, ESTstat can simulate the clustering error distribution due to insufficient overlap between sibling ESTs (ISO error), and makes correction for ISO error
3. Evaluate current sequencing redundancy based on n data
4. Estimate the number of expressed genes in the underlying cDNA library(ies) based on an EST sample or multiple samples
5. Predict the number of gene capture in an additional EST sample of given size
6. Predict the sequencing redundancy at targeted EST sample size
7. Estimate the number of genes co-expressed in two libraries

Alternatively the user can input the gene cluster profile data n directly (e.g., from other clustering program without correction for clustering errors) to perform statistical analysis.

References:

1. Ji-Ping Z. Wang, Bruce G. Lindsay, James Leebens-Mack, Liying Cui, Kerr Wall, Webb C. Miller, Claude W. dePamphilis (2004a) EST Clustering Error Evaluation and Correction. Bioinformatics Abstract PDF Supplementary materials
2. Ji-Ping Z. Wang, Bruce G. Lindsay, Liying Cui, Kerr Wall, Josh Marion, Jiaxuan Zhang, Claude W. dePamphilis (2004b) Gene number estimation and gene capture prediction in EST sequencing.(submitted) PS PDF Supplementary material
3. Ji-Ping Z. Wang and Bruce G. Lindsay (2005) A penalized nonparametric maximum likelihood approach to species richness estimation. Journal of American Statistical Association. 100(471):942-959.

If you publish results from ESTstat, please cite Wang et al. 2004a, Wang et al. 2004b.

Please send your comments and suggestions or report bugs to Ji-Ping Wang at jzwang@northwestern.edu.