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miRNA Prediction

miRCarta

Submitted by ChenLiang on Tue, 01/09/2018 - 18:46

The continuous increase of available biological data as consequence of modern high-throughput technologies poses new challenges for analysis techniques and database applications. Especially for miRNAs, one class of small non-coding RNAs, many algorithms have been developed to predict new candidates from next-generation sequencing data. While the amount of publications describing novel miRNA candidates keeps steadily increasing, the current gold standard database for miRNAs - miRBase - has not been updated since June 2014.

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miRClassify

Submitted by ChenLiang on Fri, 09/02/2016 - 21:59

MicroRNA (miRNA) family is a group of miRNAs that derive from the common ancestor. Normally, members from the same miRNA family have similar physiological functions; however, they are not always conserved in primary sequence or secondary structure. Proper family prediction from primary sequence will be helpful for accurate identification and further functional annotation of novel miRNA.

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Semirna

Submitted by ChenLiang on Fri, 09/02/2016 - 21:59

Many plant genomes are already known, and new ones are being sequenced every year. The next step for researchers is to identify all of the functional elements in these genomes, including the important class of functional elements known as microRNAs (miRNAs), which are involved in posttranscriptional regulatory pathways. However, computational tools for predicting new plant miRNAs are limited, and there is a particular need for tools that can be used easily by laboratory researchers.

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SeRPeNT

Submitted by ChenLiang on Tue, 01/09/2018 - 19:03

Small non-coding RNAs (sncRNAs) are highly abundant molecules that regulate essential cellular processes and are classified according to sequence and structure. Here we argue that read profiles from size-selected RNA sequencing capture the post-transcriptional processing specific to each RNA family, thereby providing functional information independently of sequence and structure.

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BosFinder

Submitted by ChenLiang on Fri, 09/02/2016 - 21:59

MicroRNAs (miRNAs) are small non-coding RNAs that modulate gene expression transcriptionally (transcriptional activation or inactivation) and/or post-transcriptionally (translation inhibition or degradation of their target mRNAs). This phenomenon has significant roles in growth and developmental processes in plants and animals. Bos taurus is one of the most important livestock animals, having great importance in food and economical sciences and industries.

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Wgssat

Submitted by ChenLiang on Tue, 01/09/2018 - 19:14

Mining and characterization of SSR markers from whole genomes provide valuable information about biological significance of SSR distribution and also facilitate development of markers for genetic analysis. WGS-SSR Annotation Tool (WGSSAT) is a graphical user interface pipeline developed using Java Netbeans and Perl scripts which facilitates in simplifying the process of SSR mining and characterization.

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MicRooN

Submitted by ChenLiang on Fri, 09/02/2016 - 21:59

Since Ambros' discovery of small non-protein coding RNAs in the early 1990s, the past two decades have seen an upsurge in the number of reports of predicted microRNAs (miR), which have been implicated in various functions. The correlation of miRs with cancer has spurred the usage of this class of non-coding RNAs in various cancer therapies, although most of them are at trial stages. However, the experimental identification of a miR to be associated with cancer is still an elaborate, time-consuming process.

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