WOOF – Word-oriented Objective Function for Validation of Sequence Alignments

WOOF

:: DESCRIPTION

WOOF (Word-oriented objective function) is a method designed to rigourously apply the principle of visual alignment validation. WOOF does not actually make changes to a multiple sequence alignment, but is intead intended to choose the best alignment of a set of proteins from a set of such alignments that have been generated using different algorithms and parameter settings. The winning alignment is the one that best aligns a set of conserved patterns extracted using a pattern-finding approach such as TEIRESIAS. Patterns are weighted based on their statistical significance and position relative to other patterns.

::DEVELOPER

Beiko lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows / Mac OsX / Linux
Perl

:: DOWNLOAD

WOOF

:: MORE INFORMATION

Citation

Beiko, R.G., Chan, C.X., and Ragan, M.A. (2005)
A word-oriented approach to alignment validation
Bioinformatics 21: 2230-2239

PRANK 20170427 / webPRANK – Phylogeny-aware Progressive Sequence Alignment

PRANK 20170427

:: DESCRIPTION

PRANK (Probabilistic Alignment Kit) is a probabilistic multiple alignment program for DNA, codon and amino-acid sequences. PRANK is based on a novel algorithm that treats insertions correctly and avoids over-estimation of the number of deletion events. In addition, PRANK borrows ideas from maximum likelihood methods used in phylogenetics and correctly takes into account the evolutionary distances between sequences. Lastly, PRANK allows for defining a potential structure for sequences to be aligned and then, simultaneously with the alignment, predicts the locations of structural units in the sequences.

webPRANK is an easy-to-use web interface to the PRANK alignment algorithm.

::DEVELOPER

Löytynoja Lab, Goldman Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / MacOsX / Windows

:: DOWNLOAD

PRANK

:: MORE INFORMATION

Citation:

Phylogeny-aware alignment with PRANK.
Löytynoja A.
Methods Mol Biol. 2014;1079:155-70. doi: 10.1007/978-1-62703-646-7_10.

BMC Bioinformatics. 2010 Nov 26;11:579. doi: 10.1186/1471-2105-11-579.
webPRANK: a phylogeny-aware multiple sequence aligner with interactive alignment browser.
Löytynoja A, Goldman N.

The effects of alignment error and alignment filtering on the sitewise detection of positive selection.
Jordan G, Goldman N.
Mol Biol Evol. 2012 Apr;29(4):1125-39. Epub 2011 Nov 1.

NW 3.12 – Pairwise Needleman and Wunsch Sequence Alignment program

NW 3.12

:: DESCRIPTION

NW is an implementation of the Needleman and Wunsch dynamic programming sequence alignment algorithm. It reads PIR format sequence files and reports sequence similarity calculated in a number of different ways. Optionally it can generate a PIR format alignment file.

::DEVELOPER

Andrew C.R. Martin’s Bioinformatics Group at UCL

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

:: MORE INFORMATION

JSAV 2.0 – JavaScript Sequence Alignment Viewer

JSAV 2.0

:: DESCRIPTION

JSAV is a sequence alignment viewer written purely in JavaScript. It is extremely easy to include it in your code, but has many configuration options allowing you to control the functionality available to the user of your web site.

::DEVELOPER

Andrew C.R. Martin’s Bioinformatics Group at UCL

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows / Linux/ MacOsX
JavaScript

:: DOWNLOAD

JSAV

:: MORE INFORMATION

Citation

F1000Res. 2014 Oct 23;3:249. doi: 10.12688/f1000research.5486.1. eCollection 2014.
Viewing multiple sequence alignments with the JavaScript Sequence Alignment Viewer (JSAV).
Martin AC

STRIKE 1.2 – Sequence Alignment Scoring Tool

STRIKE 1.2

:: DESCRIPTION

STRIKE (Single sTRucture Induced Evaluation) is a program to evaluate protein multiple sequence alignments using a single protein structure.

::DEVELOPER

Notredame’s Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

STRIKE

:: MORE INFORMATION

Citation:

Bioinformatics. 2011 Dec 15;27(24):3385-91. doi: 10.1093/bioinformatics/btr587. Epub 2011 Oct 28.
STRIKE: evaluation of protein MSAs using a single 3D structure.
Kemena C, Taly JF, Kleinjung J, Notredame C.

FOLDALIGN 2.5.2 / FOLDALIGNM 1.0.2 – RNA Structure and Sequence Alignment

FOLDALIGN 2.5.2 / FOLDALIGNM 1.0.2

:: DESCRIPTION

FOLDALIGN: Pairwise local and global structural alignment of RNA sequences.

FOLDALIGNM: Multiple glo-bal struc-tu-ral a-lign-ment of RNA se-quences

::DEVELOPER

Center for non-coding RNA in Technology and Health (RTH)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

FOLDALIGN , FOLDALIGNM

:: MORE INFORMATION

Citation:

Foldalign 2.5: multithreaded implementation for pairwise structural RNA alignment.
Sundfeld D, Havgaard JH, de Melo AC, Gorodkin J.
Bioinformatics. 2015 Dec 24. pii: btv748.

Fast Pairwise Structural RNA Alignments by Pruning of the Dynamical Programming Matrix,
Havgaard JH, Torarinsson E, Gorodkin J. PLOS computational biology. 3:e193, 2007

Multiple structural alignment and clustering of RNA sequences,
Torarinsson E, Havgaard JH, Gorodkin J. Bioinformatics. 23:926-32, 2007

Exonerate 2.2 – Generic Tool for Sequence Alignment

Exonerate 2.2

:: DESCRIPTION

exonerate is a generic tool for pairwise sequence comparison.It allows you to align sequences using a many alignment models, using either exhaustive dynamic programming, or a variety of heuristics.

::DEVELOPER

Guy Slater

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows with cygwin/Mac OsX/ Linux

:: DOWNLOAD

Exonerate

:: MORE INFORMATION

Citation

Guy St C Slater and Ewan Birney
Automated generation of heuristics for biological sequence comparison
BMC Bioinformatics 2005, 6:31doi:10.1186/1471-2105-6-31

MOSAL v.1 – Multiobjective Sequence Alignment

MOSAL v.1

:: DESCRIPTION

MOSAL is a program for computing the Pareto optimal alignments for the bicriteria pairwise sequence alignment. It allows the use of substitution matrices.

::DEVELOPER

Luís Paquete

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

MOSAL

:: MORE INFORMATION

Citation

M.Abbasi, L. Paquete, A.Liefooghe, M. Pinheiro and P.Matias,
Improvements on bicriteria pairwise sequence alignment: algorithms and applications,
Bioinformatics (2013) 29 (8): 996-1003.

SWCuda 1.92 – CUDA compatible for Smith-Waterman Sequence Alignment

SWCuda 1.92

:: DESCRIPTION

SWCuda (SmithWaterman-CUDA)allows to perform alignments between one or more sequences and a database (all the sequences, even in the DB, are intended to be proteinic). It is implemented in the recently released CUDA programming environment by NVidia.

::DEVELOPER

Svetlin A. Manavski, Giorgio Valle,

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
C++ compiler
NVIDIA CUDA SDK

:: DOWNLOAD

SWCuda

:: MORE INFORMATION

Citation

Svetlin A. Manavski, Giorgio Valle,
“CUDA compatible GPU cards as efficient hardware accelerators for Smith-Waterman sequence alignment“,
BMC Bioinformatics 2008, 9(Suppl 2):S10 (26 March 2008)

YAP – Pairwise Sequence Alignment Using Secondary Structures

YAP

:: DESCRIPTION

YAP (Yet Another Alignment Program) have the possibility of aligning two sequences of amino acids taking into account different properties, namely secondary structures, transmembranicity etc.

::DEVELOPER

Piero Fariselli

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
C Compiler

:: DOWNLOAD

YAP

:: MORE INFORMATION