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Links tagged with 'viral rna'

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IRESiteDatabase Content

http://www.iresite.org [open in a new window]

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RNA > Databases

The IRESite presents carefully curated experimental evidence of many eukaryotic viral and cellular internal ribosome entry site (IRES) regions. The IRESite tool provides biologically meaningful information regarding the IRESs and their experimental background (including annotation of IRES secondary structures and IRES trans-acting factors). RNA secondary structures and for searching through the structures currently stored in the database can also be done.

links directory index: 14
TitlePublication YearGoogle Scholar Citation Count
IRESite--a tool for the examination of viral and cellular internal ribosome entry sites201014
NAR Database Issue 2010
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tagsanimals computational biology dna sequence analysis genetic databases humans nucleic acid conformation nucleic acid databases plasmids ribosomes translational peptide chain initiation viral genome viral rna

PKNOTSTool Content

ftp://selab.janelia.org/pub/software/pknots/ [open in a new window]

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RNA > Structure Prediction, Visualization, and Design

Predict pseudoknot structures in RNA sequence; source code only.

links directory index: 546
TitlePublication YearGoogle Scholar Citation Count
A dynamic programming algorithm for RNA structure prediction including pseudoknots1999546
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tagsalgorithms genetic models hiv reverse transcriptase nucleic acid conformation rna thermodynamics transfer rna viral rna

pknotsRGTool Content

http://bibiserv.techfak.uni-bielefeld.de/pknotsrg/ [open in a new window]

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RNA > Structure Prediction, Visualization, and Design

pknotsRG is a server for single sequence RNA secondary structure prediction including pseudoknots; source code, binary executable, and web service available.

links directory index: 240
TitlePublication YearGoogle Scholar Citation Count
pknotsRG: RNA pseudoknot folding including near-optimal structures and sliding windows200747
Design, implementation and evaluation of a practical pseudoknot folding algorithm based on thermodynamics2004193
NAR Web Server Issue 2007
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tagsalgorithms computational biology computer simulation genetic models hepatitis delta virus nucleic acid conformation predictive value of tests programming languages rna statistical models thermodynamics viral rna

RepTarDatabase Content

http://reptar.ekmd.huji.ac.il [open in a new window]

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RNA > Databases

RepTar is a database of miRNA target predictions, based on the RepTar algorithm that is independent of evolutionary conservation considerations and is not limited to seed pairing sites.

links directory index: 5
TitlePublication YearGoogle Scholar Citation Count
RepTar: a database of predicted cellular targets of host and viral miRNAs20115
NAR Database Issue 2011
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tags3' untranslated regions algorithms animals binding sites gene expression regulation humans mice micrornas nucleic acid databases rna sequence analysis viral rna

siVirusTool Content

http://sivirus.rnai.jp/ [open in a new window]

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DNA > Tools For the Bench
Expression > Gene Regulation
Model Organisms > Other Organisms
RNA > Structure Prediction, Visualization, and Design

siVirus aids in the design of short interfering RNA (siRNA) and helps to identify conserved target sequences for antiviral RNA interference.

links directory index: 17
TitlePublication YearGoogle Scholar Citation Count
siVirus: web-based antiviral siRNA design software for highly divergent viral sequences200617
NAR Web Server Issue 2006
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tagsanti-hiv agents antiviral agents base sequence conserved sequence genetic variation rna interference rna viruses small interfering rna viral rna

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