ShRNAPred (version 1.0): An open source and standalone software for short hairpin RNA (shRNA) prediction.

ABSTRACT:

Unlabelled

The small hairpin RNAs (shRNA) are useful in many ways like identification of trait specific molecular markers, gene silencing and characterization of a species. In public domain, hardly there exists any standalone software for shRNA prediction. Hence, a software shRNAPred (1.0) is proposed here to offer a user-friendly Command-line User Interface (CUI) to predict 'shRNA-like' regions from a large set of nucleotide sequences. The software is developed using PERL Version 5.12.5 taking into account the parameters such as stem and loop length combinations, specific loop sequence, GC content, melting temperature, position specific nucleotides, low complexity filter, etc. Each of the parameters is assigned with a specific score and based on which the software ranks the predic

SUBMITTER: Singh N 

PROVIDER: S-EPMC3400981 | biostudies-literature | 2012

REPOSITORIES: biostudies-literature