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Links tagged with 'plant rna'

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miRUTool Content

http://bioinfo.noble.org/gateway/index.php?option=com_content&task=view&id=53&It...

Expression > Gene Regulation
RNA > Functional RNAs

miRU is a tool that takes as an input a small miRNA sequence and then searches for complementary matches in TIGR plant-specific gene data sets to predict potential target genes.

NAR Web Server Issue 2005
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tagsalgorithms base pair mismatch messenger rna micrornas plant genes plant rna rna sequence analysis

Netgene2Tool Content

http://www.cbs.dtu.dk/services/NetGene2/

Expression > Splicing

The NetGene2 server is a service producing neural network predictions of splice sites in human, C. elegans and A. thaliana DNA.

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tagsalgorithms arabidopsis artificial intelligence exons expert systems factual databases forecasting genetic models green fluorescent proteins introns luminescent proteins molecular sequence data neural networks (computer) plant dna plant rna reproducibility of results rna precursors rna splicing

PmiRKBDatabase Content

http://bis.zju.edu.cn/pmirkb/

Model Organisms > Databases

Plant miRNA knowledge base (PmiRKB) provides four major functional modules. In the 'SNP' module, single nucleotide polymorphism (SNP) data of seven Arabidopsis (Arabidopsis thaliana) accessions and 21 rice (Oryza sativa) subspecies were collected to inspect the SNPs within pre-miRNAs (precursor microRNAs) and miRNA-target RNA duplexes. A second module, 'Pri-miR', can be used to investigate the tissue-specific, transcriptional contexts of pre- and pri-miRNAs (primary microRNAs), based on massively parallel signature sequencing data. The third module, 'MiR-Tar', was designed to validate thousands of miRNA-target pairs by using parallel analysis of RNA end (PARE) data. The fourth module, 'Self-reg', also used PARE data to investigate the metabolism of miRNA precursors, including precursor processing and miRNA- or miRNA*-mediated self-regulation effects on their host precursors.

NAR Database Issue 2011
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tagsarabidopsis gene expression regulation knowledge bases micrornas nucleic acid databases oryza sativa plant rna rna precursors rna sequence analysis single nucleotide polymorphism

psRNATargetTool Content

http://plantgrn.noble.org/psRNATarget/.

Model Organisms > Plants
RNA > Functional RNAs

psRNATarget is a plant small RNA target analysis server which features reverse complementary matching between small RNA and target transcript, and target site accessibility evaluation. It is designed for high-throughput analysis of next generation data, and outputs a comprehensive list of small RNA-target pairs.

NAR Web Server Issue 2011
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tagsmessenger rna micrornas plant gene expression regulation plant rna rna sequence analysis small interfering rna small untranslated rna

pssRNAMinerTool Content

http://bioinfo3.noble.org/pssRNAMiner/

Model Organisms > Plants
RNA > Functional RNAs

pssRNAMiner is a web server which identifies trans-acting siRNA clusters in plants, as well as their potential phase initiators. Users input a small RNA dataset and specify a transcript-genomic library for mapping.

NAR Web Server Issue 2008
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tagsgenomics micrornas plant gene expression regulation plant rna small interfering rna