Nexalign 1.35 – Aligns Sequences to Databases

Nexalign 1.35

:: DESCRIPTION

Nexalign is a program to align millions of short reads from next-generation sequencing data sets to reference genomes.

::DEVELOPER

FANTOM

:: SCREENSHOTS

N/A

: REQUIREMENTS

  • Linux

:: DOWNLOAD

 Nexalign

:: MORE INFORMATION

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’sDepartment 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

Phylo

:: 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

 NO

:: 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

 NO

:: 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.

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.

SMALT 0.7.6 – Align DNA Sequencing Reads with Genomic Reference Sequences

SMALT 0.7.6

:: DESCRIPTION

SMALT efficiently aligns DNA sequencing reads with genomic reference sequences.

::DEVELOPER

Hannes Ponstingl.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 SMALT

:: MORE INFORMATION

BlastAlign 1.4 – Use Blast to Align Problematic Nucleotide Sequences

BlastAlign 1.4

:: DESCRIPTION

BlastAlign uses NCBI Blast to align nucleotide sequences that have large indels (INsertions/DELetions) or are otherwise difficult to align globally. The program selects the most representative sequence from the input sequences and then extracts the blast query anchored multiple alignment (in NEXUS and Phylip formats). Alternatively, the user can choose which sequence to use as an anchor. The program also outputs a matrix representing regions of homology along the sequences, which can be used to visually identify subgroups sharing particular large indels. An additional program, BlastAlignP uses tblastn to align nucleotide sequences to a single amino acid reference sequence, allowing an open reading frame to be maintained in the multiple alignment.

::DEVELOPER

Aris Katzourakis and Robert Belshaw

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

BlastAlign

:: MORE INFORMATION

Citation:

Belshaw R, Katzourakis A. 2005.
BlastAlign: a program that uses blast to align problematic nucleotide sequences.
Bioinformatics 21:122-3

LASTZ 1.03.73 – Program for Aligning DNA Sequences

LASTZ 1.03.73

:: DESCRIPTION

LASTZ is a program for aligning DNA sequences, a pairwise aligner. Originally designed to handle sequences the size of human chromosomes and from different species, it is also useful for sequences produced by NGS sequencing technologies such as Roche 454.

::DEVELOPER

Miller Lab at Penn State University Center for Comparative Genomics and Bioinformatics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  LASTZ

:: MORE INFORMATION

Citation:

Harris, R.S. (2007)
Improved pairwise alignment of genomic DNA.
Ph.D. Thesis, The Pennsylvania State University.

PASS 2.28 – Align Short Sequences

PASS 2.28

:: DESCRIPTION

PASS performs fast gapped and ungapped alignments of short DNA sequences onto a reference DNA, typically a genomic sequence. It is designed to handle a huge amount of reads such as those generated by Solexa, SOLiD or 454 technologies. The algorithm is based on a data structure that holds in RAM the index of the genomic positions of “seed” words (typically 11-12 bases) as well as an index of the precomputed scores of short words (typically 7-8 bases) aligned against each other.

::DEVELOPER

Davide Campagna

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 PASS

:: MORE INFORMATION

Citation:

Bioinformatics. 2013 Jan 15;29(2):268-70. doi: 10.1093/bioinformatics/bts675. Epub 2012 Nov 17.
PASS-bis: a bisulfite aligner suitable for whole methylome analysis of Illumina and SOLiD reads.
Campagna D1, Telatin A, Forcato C, Vitulo N, Valle G.

Bioinformatics. 2009 Apr 1;25(7):967-8. Epub 2009 Feb 13.
PASS: a program to align short sequences.
Campagna D, Albiero A, Bilardi A, Caniato E, Forcato C, Manavski S, Vitulo N, Valle G.