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|Alternative name||Nucleic Acids Phylogenetic Profiling|
|Interface||Web user interface|
|Restrictions to use||None|
Publication for Nucleic Acids Phylogenetic Profiling
Genome Wide Detection of Small Regulatory RNAs in Deep Sea Bacterium Shewanella piezotolerans WP3
[…] look for conserved sRNAs.sRNAscanner, The sRNAscanner is a computational tool used to detect the intergenic small RNA specific transcriptional units (TU) in the completely sequenced bacterial genome.NAPP (Nucleic acid phylogenetic profiling), is a clustering method that efficiently identifies non-coding RNA (ncRNA) elements in a bacterial genome.Rfam, The Rfam database is a collection of RNA fami […]
Bioinformatics of prokaryotic RNAs
[…] nment reliability scores computed by LocARNA-P not only improves the boundary prediction by more than a factor of three but also halves the FDR.A completely different comparative approach is taken by NAPP. First, it determines the phylogenetic distribution of conserved sequence elements as well as annotated protein-coding genes. Coherent phylogenetic distribution and co-occurrence in clusters of c […]
Computational Small RNA Prediction in Bacteria
[…] studies were also found in those phylogenetically conserved regions. Based on these intergenic conservation profiles, a computational protocol was developed to compute sRNA elements in bacteria. Both NAPP and PsRNA methods efficiently predict the intergenic regions of sRNAs without any precise start and ends. Due to this unique nature, we have categorized them under the ab initio group, though the […]
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