psRNA Target: a plant small RNA target analysis server (2017 release)

psRNA Target: a plant small RNA target analysis server (2017 release)

2018 | Xinbin Dai, Zhaohong Zhuang and Patrick Xuechun Zhao
psRNATarget is a web server for analyzing plant small RNA (sRNA) targets, including microRNAs (miRNAs) and phased siRNAs (phasiRNAs). It uses a scoring schema to identify complementary matches between sRNA and mRNA sequences, and evaluates target site accessibility. The 2017 release improves performance by introducing a new scoring schema that increases 'recall rate' without significantly increasing prediction output. It also allows users to customize scoring parameters for both canonical and noncanonical targets. The server now supports large data uploads and analysis through multi-threaded chunked file uploading and enhanced computing resources. The updated interface is user-friendly and provides clear, concise data. psRNATarget is freely available at http://plantgrn.noble.org/psRNATarget/. The new scoring schema (V2) covers more validated miRNA-mRNA interactions than the previous version (V1). It extends the seed region to 2-13 bp, allows two mismatches, and adjusts penalties for gaps. The server was tested with an Arabidopsis benchmark dataset, where it achieved a 6% higher recall rate than the 2011 version. It also performed well on a rice benchmark dataset, achieving an 82.7% recall rate. The new psRNATarget can handle large datasets, thanks to improved computing capacity and multi-threaded data uploading. It is more efficient than other tools like TargetFinder and TAPIR in terms of recall rate and precision. The server is now one of the best choices for analyzing plant miRNA target genes.psRNATarget is a web server for analyzing plant small RNA (sRNA) targets, including microRNAs (miRNAs) and phased siRNAs (phasiRNAs). It uses a scoring schema to identify complementary matches between sRNA and mRNA sequences, and evaluates target site accessibility. The 2017 release improves performance by introducing a new scoring schema that increases 'recall rate' without significantly increasing prediction output. It also allows users to customize scoring parameters for both canonical and noncanonical targets. The server now supports large data uploads and analysis through multi-threaded chunked file uploading and enhanced computing resources. The updated interface is user-friendly and provides clear, concise data. psRNATarget is freely available at http://plantgrn.noble.org/psRNATarget/. The new scoring schema (V2) covers more validated miRNA-mRNA interactions than the previous version (V1). It extends the seed region to 2-13 bp, allows two mismatches, and adjusts penalties for gaps. The server was tested with an Arabidopsis benchmark dataset, where it achieved a 6% higher recall rate than the 2011 version. It also performed well on a rice benchmark dataset, achieving an 82.7% recall rate. The new psRNATarget can handle large datasets, thanks to improved computing capacity and multi-threaded data uploading. It is more efficient than other tools like TargetFinder and TAPIR in terms of recall rate and precision. The server is now one of the best choices for analyzing plant miRNA target genes.
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