ESAP plus

ESAP Plus is a web-based bioinformatic pipeline designed to assist researchers in developing simple sequence repeat markers from a large EST (Expressed Sequence Tags) collection. Simple sequence repeats, also known as microsatellites, have become widely used as molecular markers in plant genetic studies due to their abundance, high allelic variation at each locus, and simplicity of analyzing using conventional PCR amplification. However, identifying SSR markers from an extensive in-house or public EST collection requires a computational pipeline that uses several standard bioinformatic tools to design high-quality EST-SSR primers.

ESAP Plus incorporates several bioinformatic scripts and standard software tools necessary for the four main procedures of EST-SSR marker development, namely pre-processing, clustering and assembly, SSR mining, and SSR primer design. ESAP Plus provides two alternative steps for reducing EST redundancy and identifying SSR loci. Using public sugarcane ESTs, ESAP Plus automatically executes the computational pipeline via a simple web user interface, which was implemented using standard PHP, HTML, CSS, and Java scripts.

With ESAP Plus, users can upload raw EST data and choose various filtering options and parameters to analyze each of the four main procedures through the web interface. All input EST data and their predicted SSR results are stored in the ESAP Plus MySQL database. Users are notified via email when the automatic process is completed, and they can download all the results through the web interface.

ESAP Plus is a comprehensive and convenient web-based bioinformatic tool for SSR marker development. It offers all necessary EST-SSR development processes with various adjustable options that users can easily use to identify SSR markers from a large EST collection. With a familiar web interface, users can upload the raw EST using the data submission page and visualize/download the corresponding EST-SSR information from within ESAP Plus. ESAP Plus can handle considerably large EST datasets.