RNAsifter 1.0 – RNA Shape Index Filter

RNAsifter 1.0

:: DESCRIPTION

RNAsifter is a non-rigorous filter for the rfam database, that is based on the abstract shape approach. It exploits the familily specific secondary structure, i.e. it computes shapes for the query-sequence and compares them to a precalculated shape-index. The exact matches deliver – hopefully only few – candiate families in which the query-sequence might fold. Membership for the candidate families is checked with the program cmsearch, afterwards.

::DEVELOPER

S. Janssen, J. Reeder and R. Giegerich.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / Mac OsX
  • perl

:: DOWNLOAD

RNAsifter

:: MORE INFORMATION

Citation

S. Janssen, J. Reeder and R. Giegerich.
Shape based indexing for faster search of RNA family databases.
BMC Bioinformatics. 2008 Feb 29;9:131.

Sparcl – Arbitrary Shape Clustering

Sparcl

:: DESCRIPTION

Sparcl finds shape-based clusters. It uses a two step approach: in the first step we select a relatively large number of candidate centroids (via ROBIN) to find seed clusters via the K-means algorithm and in the second step we use a novel similarity kernel to merge the initial seed clusters to yield the final arbitrary shaped clusters.

::DEVELOPER

Mohammed J. Zaki

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

Sparcl

:: MORE INFORMATION

Citation

Vineet Chaoji, Mohammad Al Hasan, Saeed Salem and Mohammed J. Zaki (2009)
SPARCL: An Effective and Efficient Algorithm for Mining Arbitrary Shape-based Clusters.
Knowledge and Information Systems, 21(2), Nov, pp.201-229.

RNAsc – RNA Secondary Structure Prediction using SHAPE or inline-probing data

RNAsc

:: DESCRIPTION

RNAsc is a web server that computes RNA secondary structure with user-input chemical/enzymatic probing data, especially Selective 2′-hydroxyl acylation analyzed by primer extension (SHAPE) or inline-probing data

::DEVELOPER

Clote Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 RNAsc

:: MORE INFORMATION

Citation:

PLoS One. 2012;7(10):e45160. doi: 10.1371/journal.pone.0045160. Epub 2012 Oct 16.
Integrating chemical footprinting data into RNA secondary structure prediction.
Zarringhalam K1, Meyer MM, Dotu I, Chuang JH, Clote P.

Omokage search – Shape Similarity Search of Macromolecules

Omokage search

:: DESCRIPTION

Omokage search” is a shape similarity search service for 3D structures of macromolecules. By comparing global shapes, and ignoring details, similar-shaped structures are searched.

::DEVELOPER

Omokage search team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Omokage search: shape similarity search service for biomolecular structures in both the PDB and EMDB.
Suzuki H, Kawabata T, Nakamura H.
Bioinformatics. 2015 Oct 27. pii: btv614.

regshape v1.0 – DNA Shape-based Classifier for Regulatory Elements(R pkg)

regshape v1.0

:: DESCRIPTION

The regshape R package  provides a classifier for predicting whether a given oligonucleotide sequence (of length l bp, where l would typically vary from six to as high as 25 bp) is, or is not, a transcription factor (TF) binding site.

::DEVELOPER

The Ramsey Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux
  • R

:: DOWNLOAD

 regshape

:: MORE INFORMATION

Citation

Bioinformatics. 2015 Jun 30. pii: btv391
A DNA shape-based regulatory score improves position-weight matrix-based recognition of transcription factor binding sites.
Yang J, Ramsey SA.

RNAexinv – Extended Inverse RNA Folding from Shape and Physical Attributes to Sequences

RNAexinv

:: DESCRIPTION

RNAexinv is an interactive java application that performs RNA sequence design, constrained to yield a specific RNA shape and physical attributes.

::DEVELOPER

RNAexinv team

:: SCREENSHOTS

RNAexinv

:: REQUIREMENTS

  • Windows/Linux
  • JRE

:: DOWNLOAD

 RNAexinv

:: MORE INFORMATION

Citation

RNAexinv: An extended inverse RNA folding from shape and physical attributes to sequences.
Avihoo A, Churkin A, Barash D.
BMC Bioinformatics. 2011 Aug 3;12:319. doi: 10.1186/1471-2105-12-319.

KnotShape / KnotStructure – Shape and Structure Prediction for ncRNAs including Pseudoknots

KnotShape / KnotStructure

:: DESCRIPTION

KnotShape / KnotStructure was applied to predict shapes and secondary structures on hundreds of ncRNA data sets with and without psuedoknots.

::DEVELOPER

KnotShape / KnotStructure team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 KnotShape / KnotStructure

:: MORE INFORMATION

Citation:

BMC Bioinformatics. 2013;14 Suppl 2:S1. doi: 10.1186/1471-2105-14-S2-S1. Epub 2013 Jan 21.
Shape and secondary structure prediction for ncRNAs including pseudoknots based on linear SVM.
Achawanantakun R1, Sun Y.

HypoTrace – Image Analysis Software for Measuring Hypocotyl Growth and Shape

HypoTrace

:: DESCRIPTION

HypoTrace takes time series of image files as input and output growth rate as well as hook angle measurements for Hypocotyls. The software comes with a build-in Graphical User Interface, which allows the software to be run under three modes: 1. Automatic mode with no user intervention, good for high quality images; 2. Semi-Auto mode with a little bit user intervention, good for fair quality images; 3. Manual mode, work for all images including really bad quality images. The three modes are designed to effectively detect the cotyledons bifurcation point under all conditions.

::DEVELOPER

Liya Wang

:: SCREENSHOTS

HypoTrace

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • Matlab

:: DOWNLOAD

 HypoTrace

:: MORE INFORMATION

Citation

Wang L., Uilecan I. V., Assadi A. H., Kozmik C. A., Spalding E. P.,
HypoTrace: Image Analysis Software for Measuring Hypocotyl Growth and Shape Demonstrated on Arabidopsis Seedlings Undergoing Photomorphogenesis,
Plant Physiol. 2009, 149(4), 1632-1637.

SHAPE 1.3 – Biological Shape Analysis with Elliptic Fourier Sescriptors

SHAPE 1.3

:: DESCRIPTION

SHAPE is a software for general application of the method based on EFDs. SHAPE extracts the contour shape from a full color bitmap image, delineates the contour shape with the EFDs, and finally performs the principal component analysis of the EFDs for summarizing the shape information. With the aid of this package, a researcher can easily analyze shapes on a personal computer without special knowledge about the procedures related to the method.

::DEVELOPER

IWATA, Hiroyoshi

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 SHAPE

:: MORE INFORMATION

Citation:

Iwata, H., and Y. Ukai (2002)
SHAPE: A computer program package for quantitative evaluation of biological shapes based on elliptic Fourier descriptors.
Journal of Heredity 93: 384-385.

noRNAlize 1.0 – RNA SHAPE Data Normalization software

noRNAlize 1.0

:: DESCRIPTION

noRNAlize is a data analysis package to analyze and normalize SHAPE (Selective 2′-Hydroxyl Acylation and Primer Extension) data. Traditionally, SHAPE requires the addition of a 3′ hairpin to the RNA for normalization. noRNAlize elminates the need for this experimental step by performing a global analysis of the SHAPE data, and establishing mean protection values. This is particularly important when SHAPE analysis is used to map crystal contacts in crystal structures as illustrated here.

::DEVELOPER

noRNAlize Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / MacOsX /  Linux
  • MATLAB

:: DOWNLOAD

 noRNAlize

:: MORE INFORMATION

Citation:

Vicens Q, Gooding AR, Laederach A, Cech TR,
Local RNA structural changes induced by crystallization are revealed by SHAPE,
RNA, (2007)