Gardenia – Compare & Align RNA Structures

Gardenia

:: DESCRIPTION

Gardenia is a program that Compares & aligns RNA secondary structures,without pseudoknots. The resulting alignment takes into account both the primary structure and the secondary structure.

::DEVELOPER

Bonsai Bioinformatics – INRIA

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows / Linux / MacOsX
C Complier

:: DOWNLOAD

Gardenia

:: MORE INFORMATION

Citation

Guillaume Blin, Alain Denise, Serge Dulucq, Claire Herrbach, Helene Touzet
Alignment of RNA structures
IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2008

GLASS – Aligns large Orthologous Genomic Regions

GLASS

:: DESCRIPTION

GLASS (GLobal Alignment SyStem) is a tool for aligning pairs of homologous sequences. It is designed for aligning long, divergent sequences, that contain blocks of moderate to strong homology, such as orthologous/paralogous pairs of genes

::DEVELOPER

Berger Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web Browser

:: DOWNLOAD

GLASS

:: MORE INFORMATION

Citation:

S. Batzoglou, L. Pachter, J.P. Mesirov, B. Berger, and E.S. Lander.
“Human and mouse Gene Structure: Comparative Analysis and Application to Exon Prediction.”
Genome Research, July 1, 2000.

LGSFAligner 01 – Align two RNA Secondary Structures Locally

LGSFAligner 01

:: DESCRIPTION

LGSFAligner (Local Gapped Subforest Aligner) is a tool to Align two RNA Secondary Structures Locally

::DEVELOPER

LGSFAligner team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux/Windows/MacOsX
Java

:: DOWNLOAD

LGSFAligner

:: MORE INFORMATION

Citation:

J Comput Biol. 2006 Apr;13(3):702-18.
Local gapped subforest alignment and its application in finding RNA structural motifs.
Jansson J, Hieu NT, Sung WK.

ShaEP 1.3.0 – Align Two Rigid 3D Molecular Structure Models

ShaEP 1.3.0

:: DESCRIPTION

ShaEP aligns (superimposes) two rigid 3D molecular structure models and computes a similarity index for the overlay. It can be used for the virtual screening of libraries of chemical structures against a known active molecule, or as a preparative step for 3D QSAR methods.

::DEVELOPER

Structural Bioinformatics Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows / Linux / MacOsX

:: DOWNLOAD

ShaEP

:: MORE INFORMATION

Citation:

Mikko J. Vainio, J. Santeri Puranen and Mark S. Johnson (2009)
ShaEP: Molecular Overlay Based on Shape and Electrostatic Potential.
J. Chem. Inf. Model. 49, 492-502.

Alignancer 0.6 – Align Unaligned Regions in a HMMer-3 output alignments

Alignancer 0.6

:: DESCRIPTION

Alignancer is a tool for alignment enhancing. It is performing additional alignments on masked sections of hmmalign (HMMER 3.0) multiple alignments. ClustalW (default) or Muscle is being utilized to automatically align all sections which were not covered by a profile HMM and therefore were not aligned. In using additional aligners to complement hmmalign, compulsory loss of information may be avoided keeping the entire alignment for subsequent analyses, e.g. the calculation of phylogenetic trees.

::DEVELOPER

Bioinformatics at AWI

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux/MacOsX / Windows
Python

:: DOWNLOAD

Alignancer

:: MORE INFORMATION

ALIGN 2.0 – Pairwise Alignment

ALIGN 2.0

:: DESCRIPTION

ALIGN (Pairwise alignment) is a tool designed for performing sequence alignments in a wide variety of combinations. It implements sequence to sequence, sequence to profile and profile to profile alignments with optional support of secondary structure. Different alignment options are freely selectable and include alignment types (local, global, free-shift) and number of sub-optimal results to report.

::DEVELOPER

The BioComputing UP lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
C++ Compiler

:: DOWNLOAD

ALIGN

:: MORE INFORMATION

Citation:

Curr Drug Discov Technol. 2006 Sep;3(3):167-73.
Align: a C++ class library and web server for rapid sequence alignment prototyping.
Tosatto SC, Albiero A, Mantovan A, Ferrari C, Bindewald E, Toppo S.

SHRiMP 2.2.3 – Align Genomic Reads against Target genome

SHRiMP 2.2.3

:: DESCRIPTION

SHRiMP (SHort Read Mapping Package) is a software package for aligning genomic reads against a target genome. It was primarily developed with the multitudinous short reads of next generation sequencing machines in mind, as well as Applied Biosystem’s colourspace genomic representation.

::DEVELOPER

the Computational Biology Lab at the University of Toronto’s Department of Computer Science

:: SCREENSHOTS

Command

:: REQUIREMENTS

Linux / MacOsX

:: DOWNLOAD

SHRiMP

:: MORE INFORMATION

Citation:

Matei David1, Misko Dzamba, Dan Lister, Lucian Ilie and Michael Brudno
SHRiMP2: Sensitive yet Practical Short Read Mapping
Bioinformatics (2011) 27 (7): 1011-1012.

Phylo 3.3.2 / Open-Phylo – Gaming Framework to Align Genomic Data

Phylo 3.3.2 / Open-Phylo

:: DESCRIPTION

Phylo is a human-based computing framework applying “crowd sourcing” techniques to solve the Multiple Sequence Alignment (MSA) problem. The key idea of Phylo is to convert the MSA problem into a casual game that can be played by ordinary web users with a minimal prior knowledge of the biological context.

Open-Phylo is an open crowd-computing platform to solve the multiple sequence alignment problem.

::DEVELOPER

Computer Science and Biology at McGill

:: SCREENSHOTS

:: REQUIREMENTS

Web browser

:: DOWNLOAD

Phylo ; for iSO; for Android

:: MORE INFORMATION

Citation:

Genome Biol. 2013;14(10):R116.
Open-Phylo: a customizable crowd-computing platform for multiple sequence alignment.
Kwak D, Kam A, Becerra D, Zhou Q, Hops A, Zarour E, Kam A, Sarmenta L, Blanchette M, Waldispühl J.

PLoS One. 2012;7(3):e31362. doi: 10.1371/journal.pone.0031362. Epub 2012 Mar 7.
Phylo: a citizen science approach for improving multiple sequence alignment.
Kawrykow A1, Roumanis G, Kam A, Kwak D, Leung C, Wu C, Zarour E; Phylo players, Sarmenta L, Blanchette M, Waldispühl J.

Pro-Coffee – Aligns Homologous Promoter Regions

Pro-Coffee

:: DESCRIPTION

Pro-Coffee is a multiple aligner specifically designed for homologous promoter regions.

::DEVELOPER

Notredame’s Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web browser

:: DOWNLOAD

:: MORE INFORMATION

Citation:

Nucleic Acids Res. 2012 Apr;40(7):e52. doi: 10.1093/nar/gkr1292. Epub 2012 Jan 9.
Use of ChIP-Seq data for the design of a multiple promoter-alignment method.
Erb I, González-Vallinas JR, Bussotti G, Blanco E, Eyras E, Notredame C.

M-Coffee – Combination of Multiple Sequence Alignment Packages

M-Coffee

:: DESCRIPTION

M-Coffee is a multiple sequence alignment Package. It is part of the T-Coffee distribution. The specificity of M-Coffee is that rather than computing a multiple sequence alignment on its own, it uses other packages to compute the alignments. It then uses T-Coffee to combine all these alignents into one unique final alignment.

::DEVELOPER

Notredame’s Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

M-Coffee: combining multiple sequence alignment methods with T-Coffee.
Wallace IM, O’Sullivan O, Higgins DG, Notredame C.
Nucleic Acids Res. 2006 Mar 23;34(6):1692-9. Print 2006.

The M-Coffee web server: a meta-method for computing multiple sequence alignments by combining alternative alignment methods.
Moretti S, Armougom F, Wallace IM, Higgins DG, Jongeneel CV, Notredame C.
Nucleic Acids Res. 2007 Jul;35(Web Server issue):W645-8. Epub 2007 May 25.