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Perl is a family of high-level, general-purpose, interpreted, dynamic programming languages. The languages in this family include Perl 5 and Perl 6. [Source: Wikipedia ]

AmiRNA Designer

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

MicroRNAs (miRNAs) are small non-coding RNAs that have been found in most of the eukaryotic organisms. They are involved in the regulation of gene expression at the post-transcriptional level in a sequence specific manner. MiRNAs are produced from their precursors by Dicer-dependent small RNA biogenesis pathway. Involvement of miRNAs in a wide range of biological processes makes them excellent candidates for studying gene function or for therapeutic applications. For this purpose, different RNA-based gene silencing techniques have been developed.

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Average: 4.5 (2 votes)

Mirin

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

Exploring microRNA (miRNA) regulations and protein-protein interactions could reveal the molecular mechanisms responsible for complex biological processes. Mirin is a web-based application suitable for identifying functional modules from protein-protein interaction networks regulated by aberrant miRNAs under user-defined biological conditions such as cancers. The analysis involves combining miRNA regulations, protein-protein interactions between target genes, as well as mRNA and miRNA expression profiles provided by users.

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Average: 5 (2 votes)

MiRE

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

To provide a set of useful analysis tools for the researchers to explore the microRNA data.
The R language was used for generating the Graphical Users Interface and implementing most functions. Some Practical Extraction and Report Language (Perl) scripts were used for parsing source files.

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Average: 5 (2 votes)

TissGDB

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

Tissue-specific gene expression is critical in understanding biological processes, physiological conditions, and disease. The identification and appropriate use of tissue-specific genes (TissGenes) will provide important insights into disease mechanisms and organ-specific therapeutic targets.

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Average: 5 (1 vote)

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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Average: 5 (1 vote)

comTAR

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

MicroRNAs (miRNAs) are major regulators of gene expression in plants and animals. They recognize their target messenger RNAs (mRNAs) by sequence complementarity and guide them to cleavage or translational arrest. So far, the prediction of plant miRNA-target pairs generally relies on the use of empirical parameters deduced from known miRNA-target interactions.

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Average: 5 (1 vote)

Carnation DB

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

The whole-genome sequence of carnation (Dianthus caryophyllus L.) cv. 'Francesco' was determined using a combination of different new-generation multiplex sequencing platforms. The total length of the non-redundant sequences was 568,887,315 bp, consisting of 45,088 scaffolds, which covered 91% of the 622 Mb carnation genome estimated by k-mer analysis. The N50 values of contigs and scaffolds were 16,644 bp and 60,737 bp, respectively, and the longest scaffold was 1,287,144 bp. The average GC content of the contig sequences was 36%.

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Average: 5 (1 vote)

RiceChip

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

Rice (Oryza sativa) feeds over half of the global population. A web-based integrated platform for rice microarray annotation and data analysis in various biological contexts is presented, which provides a convenient query for comprehensive annotation compared with similar databases. Coupled with existing rice microarray data, it provides online analysis methods from the perspective of bioinformatics.

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Average: 5 (1 vote)

MDTE DB

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

MicroRNAs are crucial regulators of gene expression at post-transcriptional level. Understanding origin and evolution of miRNAs and their functions. Transposable elements (TEs) provide a natural mechanism for the origin of new miRNAs derived from TEs (MDTEs) were collected to contruct a database named MDTE database (MDTE DB) for storing, searching and analyzing MDTEs. The database proveds a convenient source for studying the origin and evolution of miRNAs.[1]

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Average: 5 (1 vote)

DREAM

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

detecting RNA editing associated with microRNAs, is a webserver for the identification of mature microRNA editing events using deep sequencing data. Raw microRNA sequencing reads can be provided as input, the reads are aligned against the genome and custom scripts process the data, search for potential editing sites and assess the statistical significance of the findings. The output is a text file with the location and the statistical description of all the putative editing sites detected.[1]

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3
Average: 3 (2 votes)

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