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

:: 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.

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

:: 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.

regshape v1.1 – DNA Shape-based Classifier for Regulatory Elements(R pkg)

regshape v1.1

:: 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.

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

:: 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.

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.

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.

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)