scan-x

v1.1 03.04.2009

Harvard Medical School

Welcome to the scan-x search page. scan-x is a software tool designed to find motifs (identified using motif-x) within any sequence data set. The first large scale scan was performed using all available human, mouse, fly and yeast phosphorylation and acetylation data to perform a scan for undiscovered modification sites. Please cite the following: Chou MF & Schwartz D (2011). Using the scan-x Web site to predict protein post-translational modifications. Curr Protoc Bioinformatics. Chapter 13:Unit 13.16. doi:10.1002/0471250953.bi1316s36. PDF (608K) | PubMed Schwartz D, Chou MF and Church GM (2009). Predicting protein post-translational modifications using meta-analysis of proteome-scale data sets. Mol Cell Proteomics 8(2):365-79. PDF (2.4 M) | Supplemental Data | PubMed Using a part of the gene name, or a short unique fragment from your protein of interest, you may search our current prediction results for phosphorylation on your favorite proteins from Human, Mouse, Drosophila and Yeast protein databases, and for acetylation on Human protein databases. As described in the paper, each data set contains predicted hits at a certain level of specificity. Generally speaking, the higher the specificity, the lower the sensitivity and vice versa. The total number of predictions for each data set as of February 2009 are described in the text of the paper.

`select a data set to search within`	human ser/thr phosphorylation at 95% specificity human ser/thr phosphorylation at 99% specificity human tyr phosphorylation at 95% specificity human tyr phosphorylation at 99% specificity human lys acetylation at 95% specificity human lys acetylation at 99% specificity mouse ser/thr phosphorylation at 95% specificity mouse ser/thr phosphorylation at 99% specificity fly ser/thr phosphorylation at 95% specificity fly ser/thr phosphorylation at 99% specificity yeast ser/thr phosphorylation at 95% specificity yeast ser/thr phosphorylation at 99% specificity
`search by gene name*`	`(minimum of 3 characters)`
`AND/OR**`
`search by partial amino acid sequence`	`(e.g. MLPEDKE, mimumum 7 letters)`
`Searches are not case sensitive. When searching by gene name, human and mouse gene descriptions are derived from the IPI database, drosophila gene descriptions are derived from FlyBase, and yeast gene descriptions are derived from the SGD. *Providing genes AND sequence will return the union of the search results.`

PLEASE NOTE: The use of automatic query software is prohibited.

By clicking the 'Search' button, you certify that you meet the requirements specified by the following disclaimer: The software provided on this website may be used freely by users from academic and non-profit organizations. Users from the commercial sector should contact Daniel Schwartz (daniel.schwartz(at)uconn.edu).