Category: Alignment / BLAST

Alignment Benchmark – Collection of Protein Sequence Alignment Benchmarks

Alignment Benchmark

:: DESCRIPTION

Alignment Benchmark is a collection of protein sequence alignment benchmarks including BALIBASE v3, PREFAB v4, OXBENCH, and SABRE. These have been converted to a standard FASTA format that is convenient for further analysis. Accuracy scores for some selected methods are included to allow third party verification of my results.

::DEVELOPER

Robert Edgar

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

Alignment Benchmark

:: MORE INFORMATION

Citation

A paper is in submission. For now you can cite this URL: Edgar, R.C., http://www.drive5.com/bench.

PREFAB 4.0 – Protein Reference Alignment Database

PREFAB 4.0

:: DESCRIPTION

PREFAB (protein reference alignment benchmark) is a database designed for testing multiple sequence alignment methods.

::DEVELOPER

Robert Edgar

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

PREFAB

:: MORE INFORMATION

Citation

Edgar, R.C. (2010)
Quality measures for protein alignment benchmarks
Nucleic Acids Res., 2010, 1–9.

QSCORE – Multiple Alignment Scoring Software

QSCORE

:: DESCRIPTION

QSCORE is a quality scoring program that compares two multiple sequence alignments: an alignment to be evaluated (the “test” alignment) and a second alignment that is believed to be correct (the “reference” alignment).

::DEVELOPER

Robert Edgar

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

QSCORE

:: MORE INFORMATION

N/A

 

PALS 1.0 – Pairwise Alignment of Long Sequences

PALS 1.0

:: DESCRIPTION

PALS (Pairwise Aligner for Long Sequences)is public domain software that finds local alignments of long DNA sequences.

::DEVELOPER

Robert Edgar

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac OsX

:: DOWNLOAD

PALS

:: MORE INFORMATION

Citation

R.C. Edgar and E.W. Myers
PILER: identification and classification of genomic repeats.
Bioinformatics. 2005 Jun 1;21 Suppl 1:i152-i158

MUSCLE 3.8.31 – Multiple Sequence Alignment

MUSCLE 3.8.31

:: DESCRIPTION

MUSCLE is a program for creating multiple alignments of amino acid or nucleotide sequences. A range of options is provided that give you the choice of optimizing accuracy, speed, or some compromise between the two. Default parameters are those that gave the best average benchmark accuracy in my tests. However, benchmark accuracy is a rather dubious measure

MUSCLE Online version

::DEVELOPER

Robert Edgar

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / Mac OsX

:: DOWNLOAD

MUSCLE

:: MORE INFORMATION

Citation

Edgar, R.C. (2010)
Quality measures for protein alignment benchmarks
Nucleic Acids Res., 2010, 1–9.

QuickAlign 1.03 – Alignment editor for Macinthosh computers

QuickAlign 1.03

:: DESCRIPTION

QuickAlign was   a program for MacOS X and Classic MacOS designed to speed up editing of sequence alignments. It allows the simultaneous editing of many nucleotide or amino acid sequences using mouse functions and shortcuts, as well as automatic overlapping of sequence fragments, searching and sorting of sequences, and multiple alignment using ClustalX. Numerous additional features and the user interface are describedin the documentation

::DEVELOPER

Jörn Müller, Kai Müller.

:: SCREENSHOTS

:: REQUIREMENTS

  • Mac OsX

:: DOWNLOAD

QuickAlign

:: MORE INFORMATION

Citation

Müller J, Müller K
QuickAlign: A New Alignment Editor
Plant Molecular Biology Reporter 2003, 21:5

AuberGene 1.1 – Sensitive Genome Alignment Tool

AuberGene 1.1

:: DESCRIPTION

AuberGene is a genome alignment program which explores the idea of transitivity of local alignments. Even though it uses pairwise alignments generated by other genome alignment programs, it produces more sensitive and specific alignments by integrating the information from multiple genomes.

::DEVELOPER

The Centre for Integrative Bioinformatics VU

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

AuberGene Source Code

:: MORE INFORMATION

Citation

Szklarczyk, R., Heringa, J.,
AuberGene – a sensitive genome alignment tool,
Bioinformatics, 15 June 2006; 22: 1431 – 1436

ALICAO – Contact-based Sequence Alignment

ALICAO

:: DESCRIPTION

ALICAO is a program to perform contact-based sequence alignment, where the structure of the first sequence is known (template) and the sequence of the second sequence is unknown (query). A contact map is extracted from the template structure and the program aligns the two sequences by maximizing a combination of contact mutation and sequence mutation probability. The combination of structure and sequence information overall improves alignments between sequences with < 30% sequence identity.

::DEVELOPER

The Centre for Integrative Bioinformatics VU

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

ALICAO Source Code

:: MORE INFORMATION

Citation

J. Kleinjung, J. Romein, K. Lin and J. Heringa,
Contact-based sequence alignment,
Nucleic Acids Research 32(8) (2004) 2464-2473

Friend 2.0 – Multiple Structure Visualization & Multiple Sequence Alignment

Friend 2.0

:: DESCRIPTION

Friend (Integrated FRont-END) is a bioinformatics application designed for simultaneous analysis and visualization of multiple structures and sequences of proteins and/or DNA/RNA. The application provides basic functionalities such as: structure visualization with different rendering and coloring, sequence alignment, and simple phylogeny analysis, along with a number of extended features to perform more complex analyses of sequence structure relationships, including: structure alignment of proteins, investigation of specific interaction motifs, studies of protein-protein and protein-DNA interactions, and protein super-families.

::DEVELOPER

ilyin lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • Java

:: DOWNLOAD

Friend

:: MORE INFORMATION

Citation:

Friend, an integrated analytical front-end application for bioinformatics. Bioinformatics. 2005 Sep 15(18):3677-8.

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