JOY 5.0 – Protein Sequence-Structure Representation and Analysis

JOY 5.0

:: DESCRIPTION

JOY is a program to annotate protein sequence alignments with three-dimensional (3D) structural features. It was developed to display 3D structural information in a sequence alignment and help understand the conservation of amino acids in their specific local environments. For instance, it has been recognised that a sidechain hydrogen-bonded to a main-chain amide plays an important role in stabilizing the 3D structure and is generally well conserved during evolution. Such a residue is shown in a bold-face letter in the formatted alignments. Another example is the importance of solvent inaccessible residues which are shown in UPPER-CASE letters.

::DEVELOPER

the Mizuguchi Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

JOY

:: MORE INFORMATION

Citation

Mizuguchi, K., Deane, C.M., Blundell, T.L., Johnson,M.S. and Overington, J.P. (1998)
JOY: protein sequence-structure representation and analysis.
Bioinformatics 14:617-623.

ExpaRNA 1.0 – Exact Matching of Sequence-structure

ExpaRNA 1.0

:: DESCRIPTION

ExpaRNA is a fast, motif-based comparison and alignment tool for RNA molecules. Instead of computing a full sequence-structure alignment, it computes the best arrangement of sequence-structure motifs common to two RNAs. A motif is a local (or isolated) substructure which is identical to both RNAs.

::DEVELOPER

Freiburg Bioinformatics Group.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

ExpaRNA

:: MORE INFORMATION

Citation

Freiburg RNA Tools: a web server integrating IntaRNA, ExpaRNA and LocARNA
Cameron Smith, Steffen Heyne, Andreas S. Richter, Sebastian Will, Rolf Backofen
In: Nucleic Acids Research, 2010, 38 Suppl, W373-7

APTANI2 – Select Aptamers through Sequence-structure Motif analysis of HT-SELEX data

APTANI2

:: DESCRIPTION

APTANI is a computational tool to identify target-specific aptamers from HT-SELEX data and secondary structure information

::DEVELOPER

Bicciato Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
Python

:: DOWNLOAD

APTANI

:: MORE INFORMATION

Citation

APTANI: a computational tool to select aptamers through sequence-structure motif analysis of HT-SELEX data.
Caroli J, Taccioli C, De La Fuente A, Serafini P, Bicciato S.
Bioinformatics. 2015 Sep 22. pii: btv545

lara 1.3.2a – Sequence-structure Alignment of RNA Sequences

lara 1.3.2a

:: DESCRIPTION

lara (“lagrangian relaxed structural alignment”) is a tool for the sequence-structure alignment of RNA sequences.

::DEVELOPER

Life Sciences Group, Centrum Wiskunde & Informatica

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
T-Coffee

:: DOWNLOAD

lara

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2007 Jul 27;8:271.
Accurate multiple sequence-structure alignment of RNA sequences using combinatorial optimization.
Bauer M1, Klau GW, Reinert K.

ViTO 20031125 – Protein Sequence Structure Alignments

ViTO 20031125

:: DESCRIPTION

ViTO is a graphical application, including an editor, of multiple sequence alignment and a three-dimensional (3D) structure viewer. It is possible to manipulate alignments containing hundreds of sequences and to display a dozen structures. ViTO can handle so-called ‘multiparts’ alignments to allow the visualization of complex structures (multi-chain proteins and/or small molecules and DNA) and the editing of the corresponding alignment. The 3D viewer and the alignment editor are connected together allowing rapid refinement of sequence–structure alignment by taking advantage of the immediate visualization of resulting insertions/deletions and strict conservations in their structural context. More generally, it allows the mapping of informations about the sequence conservation extracted from the alignment onto the 3D structures in a dynamic way.

::DEVELOPER

V.Catherinot — CBS BioInformatic Team — labesse@cbs.cnrs.fr

:: SCREENSHOTS

:: REQUIREMENTS

Linux/WIndows/MacOsX

:: DOWNLOAD

ViTO

:: MORE INFORMATION

Citation:

ViTO: tool for refinement of protein sequence–structure alignments
Vincent Catherinot and Gilles Labesse
Bioinformatics (2004) 20 (18): 3694-3696.

Quasar 1.2 – Score & Rank Sequence-structure Alignments

Quasar 1.2

:: DESCRIPTION

Quasar (quality of sequence–structure alignments ranking) is a flexible tool for calculating quality scores of sequence-structure alignments. The main reason for its flexibility is that you do not have to write any additional Java code in order to combine single alignment quality scores (also called scoring schemes) to scoring function (done by score conductors) but you only have to provide the system a XML – like configuration file.

::DEVELOPER

Institut für Informatik, Ludwig-Maximilians-Universität München

:: SCREENSHOTS

:: REQUIREMENTS

Windows / Linux / Mac OsX
Java

:: DOWNLOAD

Quasar

:: MORE INFORMATION

Citation

Fabian Birzele, Jan Gewehr, Ralf Zimmer.
QUASAR–scoring and ranking of sequence-structure alignments.
Bioinformatics, vol 21, no. 24, pp. 4425–4426, Dec 2005.