Abstract
LSAT is a web-based microsatellite SSR marker designer tool specific for the Liliaceae family. It is developed using HTML, CSS, PHP, Perl and Java scripts. It works without extra add-ons on standard browsers. LSAT provides SSR primer designing service using the web interface. It helps in SSR mining and primer design. LSAT is user friendly with customizable search parameters producing visual output having download options. The current version of LSAT is backed by two data sets, namely, lily EST (Expressed Sequence Tag) from NCBI and lily nr (non redundant) with 4,099 and 216,768 unigenes, respectively. LSAT will be updated regularly upon availability of additional data (either EST and/or transcriptome) on Liliaceae.Availability:LSAT is available for free at http://210.110.86.160/Lsat/Lsat.html
Highlights
Microsatellite markers are extensively used in plant breeding due to its co-dominant nature, genomic abundance, and high degree of polymorphism
With the advancement of sequencing technology, large number of sequences from wide range of plant species is made available in the public domains. This is a valuable resource for designing SSR marker
It should be noted that the SSR search should be run for submitting input information to the server for processing when custom parameters are used
Summary
Microsatellite markers are extensively used in plant breeding due to its co-dominant nature, genomic abundance, and high degree of polymorphism. We describe a unique web-based LSAT tool, which is easy to handle, user friendly for SSR development It provides graphical user interface option for customizing search parameter, and output results with detail statistics can be downloaded. Caveat and future development: LSAT is freely available for use It is a user friendly, fast and a robust web-server of SSR marker specific for Liliaceae family. It provides a Graphical User Interface (GUI) with customized parameters of SSR design with known statistical information. This is the unique feature of LSAT compared to other existing SSR tools. The interface will be upgraded frequently with advanced scripts by displaying results in graphical representation having advanced features for SSR marker
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