ESAP plus: a web-based server for EST-SSR marker development.
Simple sequence repeats (SSRs) have become widely used as molecular markers in plant genetic studies due to their abundance, high allelic variation at each locus and simplicity to analyze using conventional PCR amplification. To study plants with unknown genome sequence, SSR markers from Expressed Sequence Tags (ESTs), which can be obtained from the plant mRNA (converted to cDNA), must be utilized. With the advent of high-throughput sequencing technology, huge EST sequence data have been generated and are now accessible from many public databases. However, SSR marker identification from a large in-house or public EST collection requires a computational pipeline that makes use of several standard bioinformatic tools to design high quality EST-SSR primers. Some of these computational tools are not users friendly and must be tightly integrated with reference genomic databases.



A web-based bioinformatic pipeline, called EST Analysis Pipeline Plus (ESAP Plus), was constructed for assisting researchers to develop SSR markers from a large EST collection. ESAP Plus incorporates several bioinformatic scripts and some useful standard software tools necessary for the four main procedures of EST-SSR marker development, namely 1) pre-processing, 2) clustering and assembly, 3) SSR mining and 4) SSR primer design. The proposed pipeline also provides two alternative steps for reducing EST redundancy and identifying SSR loci. Using public sugarcane ESTs, ESAP Plus automatically executed the aforementioned 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 this web interface. All input EST data and their predicted SSR results will be stored in the ESAP Plus MySQL database. Users will be notified via e-mail 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. ESAP Plus 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 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. This EST-SSR discovery tool can be accessed directly from: http://gbp.kku.ac.th/esap_plus/ .
Department of Biology, Faculty of Science, Khon Kaen University, Khon Kaen, 40002, Thailand.
Piyarat
P
Ponyared
Department of Computer Engineering, Faculty of Engineering, Khon Kaen University, Khon Kaen, 40002, Thailand.
Jiradej
J
Ponsawat
National Center for Genetic Engineering and Biotechnology (BIOTEC), Pathum Thani, 12120, Thailand.
Sissades
S
Tongsima
Department of Computer Science, Faculty of Science, Khon Kaen University, Khon Kaen, 40002, Thailand.
Pusadee
P
Seresangtakul
Department of Plant Science and Agricultural Resources, Faculty of Agriculture, Khon Kaen University, Khon Kaen, 40002, Thailand.
Chutipong
C
Akkasaeng
Department of Biology, Faculty of Science, Khon Kaen University, Khon Kaen, 40002, Thailand. naptan@kku.ac.th.
Nathpapat
N
Tantisuwichwong
D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods*; D030541:Databases, Genetic; D020224:Expressed Sequence Tags; D005819:Genetic Markers; D023281:Genomics / Q000379:methods; D018895:Microsatellite Repeats; D015203:Reproducibility of Results; D012984:Software; D064878:Web Browser; D057188:Workflow
D005819:Genetic Markers
Bioinformatics; EST-SSR development pipeline; Expressed sequence tags (ESTs); Simple sequence repeats (SSRs)