Sigma 2.0 BETA – Non-coding DNA Sequence Alignment

Sigma 2.0 BETA

:: DESCRIPTION

Sigma (Simple greedy multiple alignment) is an alignment program with a new algorithm and scoring scheme designed specifically for non-coding DNA sequence.This problem is now growing in importance with the increasing number of fully-sequenced species. In particular, studies of gene regulation seek to take advantage of comparative genomics, and recent algorithms (such as PhyloGibbs) for finding regulatory sites in phylogenetically-related intergenic sequence require alignment as a preprocessing step.

::DEVELOPER

RAHUL SIDDHARTHAN

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

Sigma

:: MORE INFORMATION

Citation:

Rahul Siddharthan,
“Sigma: multiple alignment of weakly-conserved non-coding DNA sequences“,
BMC Bioinformatics 7:143 (2006)

MALT 0.5.3 – MEGAN Alignment tool

MALT 0.5.3

:: DESCRIPTION

MALT performs alignment of metagenomic reads against a database of reference sequences (such as NR, GenBank or Silva) and produces a MEGAN RMA file as output.

::DEVELOPER

the Algorithms in Bioinformatics lab.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows / MacOsX / Linux
Java

:: DOWNLOAD

MALT

:: MORE INFORMATION

MINNOU – Membrane Protein IdeNtificatioN withOUt explicit use of Hydropathy Profiles and Alignments

MINNOU

:: DESCRIPTION

The MINNOU server can be used for predicting trans-membrane domains.

:: SCREENSHOTS

N/A

::DEVELOPER

Meller Lab

:: REQUIREMENTS

Linux

:: DOWNLOAD

MINNOU

:: MORE INFORMATION

Citation

Bioinformatics. 2006 Feb 1;22(3):303-9. Epub 2005 Nov 17.
Enhanced recognition of protein transmembrane domains with prediction-based structural profiles.
Cao B1, Porollo A, Adamczak R, Jarrell M, Meller J.

FTALIGN – Fast Topology-independent and Global Structure Alignment through an FFT-based algorithm.

FTALIGN

:: DESCRIPTION

The FTALIGN server is to align two protein structures by using a fast Fourier transformation (FFT)-based topology-independent and global structure alignment algorithm.

::DEVELOPER

Huang Laboratary

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

FTALIGN

:: MORE INFORMATION

Citation:

Wen Z, He J, Huang SY.
Topology-independent and global protein structure alignment through an FFT-based algorithm.
Bioinformatics. 2020 Jan 15;36(2):478-486. doi: 10.1093/bioinformatics/btz609. PMID: 31384919.

BitPAl – Bit-parallel Alignment

BitPAl

:: DESCRIPTION

BitPAl is a bit-parallel algorithm for general, integer-scoring global alignment. Integer-scoring schemes assign integer weights for match, mismatch, and insertion/deletion.

::DEVELOPER

Laboratory for Biocomputing and Informatics at Boston University.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
C Compiler

:: DOWNLOAD

BitPAl

:: MORE INFORMATION

Citation

BitPAl: A Bit-Parallel, General Integer-Scoring Sequence Alignment Algorithm.
Loving J, Hernandez Y, Benson G.
Bioinformatics. 2014 Jul 29. pii: btu507.

PLAST v2.3.1 – Parallel Local Alignment Search Tool for Database Comparison

PLAST v2.3.1

:: DESCRIPTION

PLAST (Parallel Local Alignment Search Tool for Database Comparison) is an intensive bank sequence comparison with a parallel version of BLAST-like software.The algorithm exploits two key parallel features of existing and future microprocessors: the SIMD programming model (SSE instruction set) and the multithreading concept (multicore). Compared to multithreaded BLAST software, tests performed on an 8-processor server have shown speedup ranging from 3 to 6 with a similar level of accuracy.

::DEVELOPER

PLAST team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows / Mac / Linux

:: DOWNLOAD

PLAST

:: MORE INFORMATION

Citation

V.H. Nguyen, D. Lavenier,
PLAST: parallel local alignment search tool for database comparison,
BMC Bioinformatics, 2009 10(329).

GASSST 1.28 – Global Alignment Short Sequence Search Tool

GASSST 1.28

:: DESCRIPTION

GASSST (Global Alignment Short Sequence Search Tool) is 2-fold—achieving high performance with no restrictions on the number of indels with a design that is still effective on long reads.

::DEVELOPER

Dominique Lavenier , Guillaume Rizk , Damien Fleury

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
GNU gcc compiler

:: DOWNLOAD

GASSST

:: MORE INFORMATION

Citation

Guillaume Rizk and Dominique Lavenier
GASSST: global alignment short sequence search tool
Bioinformatics (2010) 26 (20): 2534-2540.

NETAL – Global Alignment of Protein-protein Interaction Networks

NETAL

:: DESCRIPTION

NETAL (network aligner) is a software for the global alignment of protein-protein interaction networks. It uses a greedy method, based on the alignment scoring matrix, which is derived from both biological and topological information of input networks to find the best global network alignment.

::DEVELOPER

Somaye Hashemifar

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

NETAL

:: MORE INFORMATION

Citation:

NETAL: a new graph-based method for global alignment of protein-protein interaction networks.
Neyshabur B, Khadem A, Hashemifar S, Arab SS.
Bioinformatics. 2013 Jul 1;29(13):1654-62. doi: 10.1093/bioinformatics/btt202. Epub 2013 May 21.

Syntenator 2 – Multiple Gene Order Alignments with a Gene-specific Scoring Function

Syntenator 2

:: DESCRIPTION

Syntenator represents genomes and alignments thereof as partial order graphs (POGs). These POGs are aligned by a dynamic programming approach employing a gene-specific scoring function. The scoring function reflects the level of protein sequence similarity for each possible gene pair. Our method consistently defines larger homologous regions in pairwise gene order alignments than nucleotide-level comparisons. Our method is superior to methods that work on predefined homology gene sets (as implemented in Blockfinder). Syntenator successfully reproduces 80% of the EnsEMBL man-mouse conserved syntenic blocks. The full potential of our method becomes visible by comparing remotely related genomes and multiple genomes. Gene order alignments potentially resolve up to 75% of the EnsEMBL 1:many orthology relations and 27% of the many:many orthology relations.

::DEVELOPER

BIMSB Bioinformatics Core.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows / Mac OsX
Java

:: DOWNLOAD

Syntenator

:: MORE INFORMATION

Citation:

Algorithms Mol Biol. 2008 Nov 6;3:14.
Syntenator: multiple gene order alignments with a gene-specific scoring function.
Rödelsperger C, Dieterich C.

spinal 2 – Scalable Protein Interaction Network Alignment

spinal 2

:: DESCRIPTION

SPINAL is an algorithm for the problem of globally aligning a pair of PPI networks.

::DEVELOPER

Cesim Erten,Ahmet Emre Aladağ

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
C++ Compiler

:: DOWNLOAD

spinal

:: MORE INFORMATION

Citation

SPINAL: scalable protein interaction network alignment.
Aladag AE, Erten C.
Bioinformatics (2013) 29 (7): 917-924.