FoldNucleus – Calculation the Folding Nucleus for RNA or Protein

 3D molecular model 0 views Comments Off on FoldNucleus – Calculation the Folding Nucleus for RNA or Protein
Jul 072015
 

FoldNucleus

:: DESCRIPTION

FoldNucleus is a server  to calculate the folding nucleus for RNA molecules with known 3D structures-including pseudoknots, tRNAs, hairpins, and ribozymes-and for protein molecules with known 3D structures, as long as they are smaller than 200 amino acid residues.

::DEVELOPER

FoldNucleus team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

Bioinformatics. 2015 Jun 22. pii: btv369.
FoldNucleus: Web server for the prediction of RNA and protein folding nuclei from their 3D structures.
Pereyaslavets LB, Sokolovsky IV, Galzitskaya OV.

Bandage v0.5.6 – Navigating De novo Assembly Graphs Easily

 Assembly Tools 0 views Comments Off on Bandage v0.5.6 – Navigating De novo Assembly Graphs Easily
Jul 072015
 
Bandage v0.5.6 - Navigating De novo Assembly Graphs Easily

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Sincell 1.0.0 – Analysis of Cell State Hierarchies from Single-cell RNA-seq

 Miscellaneous 0 views Comments Off on Sincell 1.0.0 – Analysis of Cell State Hierarchies from Single-cell RNA-seq
Jul 072015
 
Sincell 1.0.0 - Analysis of Cell State Hierarchies from Single-cell RNA-seq

Sincell 1.0.0 :: DESCRIPTION Sincell is an R/Bioconductor package for statistical assessment of cell-state hierarchies from single-cell RNA-seq. ::DEVELOPER Miguel Juliá <migueljuliamolina at gmail.com>, Amalio Telenti <atelenti at jcvi.org>, :: SCREENSHOTS N/A :: REQUIREMENTS Windows/ Linux/ MacOsX Python :: DOWNLOAD  Sincell :: MORE INFORMATION Citation: Sincell: an R/Bioconductor package for statistical assessment of cell-state hierarchies […]

ernwin 0.1 – RNA Structure Prediction

 RNA Analysis 0 views Comments Off on ernwin 0.1 – RNA Structure Prediction
Jul 072015
 
ernwin 0.1 - RNA Structure Prediction

ernwin 0.1 :: DESCRIPTION ernwin is a program for sampling coarse grain 3D RNA structures. ::DEVELOPER Peter Kerpedjiev :: SCREENSHOTS N/A :: REQUIREMENTS Windows/ Linux/ MacOsX Python :: DOWNLOAD  ernwin :: MORE INFORMATION Citation: Predicting RNA 3D structure using a coarse-grain helix-centered model. Kerpedjiev P, Höner Zu Siederdissen C, Hofacker IL. RNA. 2015 Jun;21(6):1110-21. doi: […]

forna 20150415 – RNA Secondary Structure Visualization Using a Force Directed Graph Layout

 RNA Analysis 1 views Comments Off on forna 20150415 – RNA Secondary Structure Visualization Using a Force Directed Graph Layout
Jul 072015
 
forna 20150415 - RNA Secondary Structure Visualization Using a Force Directed Graph Layout

forna 20150415 :: DESCRIPTION forna is a web-based tool for displaying RNA secondary structure which allows users to easily convert sequences and secondary structures to clean, concise and customizable visualizations. ::DEVELOPER Peter Kerpedjiev :: SCREENSHOTS :: REQUIREMENTS Windows/ Linux/ MacOsX Python :: DOWNLOAD  forna :: MORE INFORMATION Citation: forna (force-directed RNA): Simple and Effective Online RNA […]

GenomeD3Plot – SVG based Genome Viewer written in Javascript using D3

 DNA / Genome Analysis 2 views Comments Off on GenomeD3Plot – SVG based Genome Viewer written in Javascript using D3
Jul 072015
 
GenomeD3Plot - SVG based Genome Viewer written in Javascript using D3

GenomeD3Plot :: DESCRIPTION GenomeD3Plot (formerly Islandplot) is an SVG based genome viewer written in javascript using D3 ::DEVELOPER Brinkman lab  :: SCREENSHOTS N/A :: REQUIREMENTS javascript :: DOWNLOAD GenomeD3Plot :: MORE INFORMATION Citation: GenomeD3Plot: A library for rich, interactive visualizations of genomic data in web applications. Laird MR, Langille MG, Brinkman FS. Bioinformatics. 2015 Jun […]

SylArray – Automated online analysis of miRNA Seed Enrichment

 RNA Analysis 0 views Comments Off on SylArray – Automated online analysis of miRNA Seed Enrichment
Jul 072015
 
SylArray - Automated online analysis of miRNA Seed Enrichment

SylArray :: DESCRIPTION SylArray is a web-based analysis resource designed to examine influence of small RNAs on expression profiles. ::DEVELOPER Enright Group :: SCREENSHOTS N/A :: REQUIREMENTS Web browser :: DOWNLOAD  NO :: MORE INFORMATION Citation: Bioinformatics. 2010 Nov 15;26(22):2900-1. doi: 10.1093/bioinformatics/btq545. Epub 2010 Sep 24. SylArray: a web server for automated detection of miRNA […]

Chimira 1.0 – Analysis of small RNA Sequencing data and microRNA modifications

 RNA Analysis 0 views Comments Off on Chimira 1.0 – Analysis of small RNA Sequencing data and microRNA modifications
Jul 072015
 
Chimira 1.0 - Analysis of small RNA Sequencing data and microRNA modifications

Chimira 1.0 :: DESCRIPTION Chimira is an online tool for analysing large amounts of small RNA-Seq data and acquiring their modifications profile. ::DEVELOPER Enright Group :: SCREENSHOTS N/A :: REQUIREMENTS Web browser :: DOWNLOAD  NO :: MORE INFORMATION Citation: Chimira: Analysis of small RNA Sequencing data and microRNA modifications. Vitsios DM, Enright AJ. Bioinformatics. 2015 […]

LFQC 1.1 – Lossless Compression Algorithm for FASTQ Files

 File Conversion 34 views Comments Off on LFQC 1.1 – Lossless Compression Algorithm for FASTQ Files
Jul 072015
 
LFQC 1.1 - Lossless Compression Algorithm for FASTQ Files

LFQC 1.1 :: DESCRIPTION LFQC is a new lossless non-reference based fastq compression algorithm. ::DEVELOPER Sanguthevar Rajasekaran :: SCREENSHOTS N/A :: REQUIREMENTS Linux Ruby :: DOWNLOAD  LFQC :: MORE INFORMATION Citation LFQC: A lossless compression algorithm for FASTQ files. Nicolae M, Pathak S, Rajasekaran S. Bioinformatics. 2015 Jun 20. pii: btv384.

DBChIP 1.12.0 – Differential Binding of Transcription Factor with ChIP-seq

 DNA / Genome Analysis 9 views Comments Off on DBChIP 1.12.0 – Differential Binding of Transcription Factor with ChIP-seq
Jul 072015
 
DBChIP 1.12.0 - Differential Binding of Transcription Factor with ChIP-seq

DBChIP 1.12.0 :: DESCRIPTION DBChIP detects differentially bound sharp binding sites across multiple conditions, with or without matching control samples. ::DEVELOPER Kun Liang :: SCREENSHOTS N/A :: REQUIREMENTS Linux /  Windows / MacOsX R BioCOnductor :: DOWNLOAD  DBChIP :: MORE INFORMATION Citation Bioinformatics. 2012 Jan 1;28(1):121-2. doi: 10.1093/bioinformatics/btr605. Epub 2011 Nov 3. Detecting differential binding […]