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

 NW

:: 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

 FOLDALIGNFOLDALIGNM

:: 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

ICM-Browser 3.8-7d – Molecules & Sequence Alignments Visualization

ICM-Browser 3.8-7d

:: DESCRIPTION

ICM-Browser provides a biologist or a chemist with direct access to the treasures of structural biology and protein families.It reads a variety of file formats directly from the database web-sites including: PDB, chemical, electron density maps, sequence and alignment files. ICM-Browser provides a rich professional molecular graphics environment with powerful representations of proteins, DNA and RNA, and multiple sequence alignments.

When you purchase the license ICM-Browser will become ICM-Browser-Pro.ICM-Browser-Pro is a high quality visualizer and annotator for three dimensional molecular structures, sequences, alignments, chemical spreadsheets and biological data. It allows you to read data from multiple file formats, annotate the data, and write multi-slide documents in a single small cross-platform file. ICM Browser Pro is well suited for creating, storing and sharing structural, biological and chemical information. The files can then be opened and viewed with the free ICM Browser.

::DEVELOPER

Molsoft LLC.

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/Linux/Mac OS X

:: DOWNLOAD

ICM-Browser ; Manual

:: MORE INFORMATION

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

elPrep 2.4 – High-Performance Preparation of Sequence Alignment/Map Files for Variant Calling

elPrep  2.4

:: DESCRIPTION

elPrep is a high-performance tool for preparing .sam/.bam/.cram files for variant calling in sequencing pipelines.It can be used as a drop-in replacement for SAMtools/Picard, and was extensively tested with different pipelines for variant analysis with GATK.

::DEVELOPER

The Exascience Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

 elPrep

:: MORE INFORMATION

Citation

PLoS One. 2015 Jul 16;10(7):e0132868. doi: 10.1371/journal.pone.0132868. eCollection 2015.
elPrep: High-Performance Preparation of Sequence Alignment/Map Files for Variant Calling.
Herzeel C, Costanza P, Decap D, Fostier J, Reumers J

SMRT Analysis 2.3.0 – Software Suite for Sequence Alignment, Assembly, Variant Detection, and Base Modification discovery

SMRT Analysis 2.3.0

:: DESCRIPTION

SMRT Analysis is a bioinformatics software suite for analyzing single molecule, real-time DNA sequencing data from Pacific Biosciences.

::DEVELOPER

Pacific Biosciences of California, Inc

:: SCREENSHOTS

SMRTAnalysis

:: REQUIREMENTS

  • Linux
  • perl
  • Java 

:: DOWNLOAD 

 SMRT Analysis

:: MORE INFORMATION

Citation

Genome Integr. 2011 Dec 20;2:10. doi: 10.1186/2041-9414-2-10.
Direct detection and sequencing of damaged DNA bases.
Clark TA, Spittle KE, Turner SW, Korlach J.