Sequence-Structure Motif Base: pre-miRNA prediction webserver




Introduction:


    Sequence-Structure Motif Base: pre-miRNA prediction webserver, mean as a free web tool for users to predict pre-miRNAs accuratelly from given sequences with the sequence-structure motif methods. Meanwhile, to the predictied pre-miRNAs, their corresponding mature miRNAs and their second-structures also can be predictied and displayed to users.


    It implements effective programs PriMir and Mirident, which were confirmed accuratelly for predicting pre-miRNA and RNAfold software for plotting their second-structures. This tool is comprised with a set of perl, python, PHP programs.


    The webserver is simpled to operate for users. You only need to put in or upload nucleotide sequence with FASTA format and set the parameters including value of sliding window size and step, the minimum free energy. The displaying second-structure and Email is optional. After your submitting, the webserver will exercise the program to predicte. Only needing a short time, the credible pre-miRNAs and their second-structures will be calculated and feedback to you. All informations are shown in your web page.

 



About
the sequence-structure motif methods :

    

    The functionality of an RNA molecule is predominantly determined by its primary nucleotides sequence and the intra-molecular interactions (hydrogen-bonding) deciding its secondary or 3-dimensional structure. These two modes of molecular information have conventionally been represented by a string of letters (e.g., UUCCCAAAGUUGAGAA) denoting the chemical composition of a 16 nucleotides long RNA molecule, and a string of brackets and dots (e.g., “(((.((….)).)))”) denoting the intra-molecular interactions forming the basis for its secondary structure. In a molecular and functional context the combination of both aspects are probably of high importance. To be able to identify molecular features which combine sequence and structural information, we therefore integrated both sequence and secondary structure into a common information string (ss-string). Replacing the structure symbols “(”, “.” and “)” by “L”, “D” and “R”, respectively, and adding these as subscripts to each respective nucleotide notation, the chemical composition and the intra-molecular structural of the above RNA molecule can be represented by a single information string, i.e., ULULCLCDCLALADADGDUDURGRADGRARAR  (“NS” denoting “any nucleotide, any intra-molecular interaction”). From these ss-strings we extracted frequently occurring motifs (ss-motifs) of varying length which were subsequently used to distinguish pre-miRNAs from other stem-loop structures.





    As one webserver predicting the pre-miRNA, we are committed to make the software available to as many scientists as possible, so the programs can all be downloaded from the download page of the site. To operate these programs in your computer, you need to install Perl, Python, SVM. To make the software more accessible to the wide scientific community, we recommendate you using the webserver that allow sequence submitting to be performed interactively via the web.


    If you have used this website, please consider citing it.

 

 

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