GibbsCluster 2.0 – Simultaneous Alignment and Clustering of Peptide data

GibbsCluster 2.0

:: DESCRIPTION

GibbsCluster is a web server for simultaneous alignment and clustering of peptide data

::DEVELOPER

DTU Health Tech

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 GibbsCluster

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Jan 1;29(1):8-14. doi: 10.1093/bioinformatics/bts621. Epub 2012 Oct 24.
Simultaneous alignment and clustering of peptide data using a Gibbs sampling approach.
Andreatta M1, Lund O, Nielsen M.

RNAmountAlign – RNA Sequence/Structure Alignment

RNAmountAlign

:: DESCRIPTION

RNAmountAlign is a novel algorithm for RNA sequence/structure pairwise alignment, that runs in O(n3) time and O(n2) space; moreover, our software returns a p-value (transformable to expect value E) based on Karlin-Altschul statistics as well as parameter fitting.

::DEVELOPER

Clote Lab 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

RNAmountAlign

:: MORE INFORMATION

Citation:

PLoS One, 15 (1), e0227177 2020 Jan 24 eCollection 2020
RNAmountAlign: Efficient Software for Local, Global, Semiglobal Pairwise and Multiple RNA Sequence/Structure Alignment
Amir H Bayegan , Peter Clote

PISwap – Protein Interaction Network Alignments

PISwap

:: DESCRIPTION

PISwap is a software for optimizing global pairwise alignments of protein interaction networks, based on a local optimization heuristic that has previously demonstrated its effectiveness for a variety of other intractable problems.

::DEVELOPER

Leonid Chindelevitch (leonidus at mit dot edu), Bonnie Berger‘s group at MIT.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Python

:: DOWNLOAD

 PISwap

:: MORE INFORMATION

Citation:

Bioinformatics. 2013 Nov 1;29(21):2765-73. doi: 10.1093/bioinformatics/btt486
Optimizing a global alignment of protein interaction networks.
Chindelevitch L, Ma CY, Liao CS, Berger B.

Harvest 1.1.2 – A Suite of Core-genome Alignment and Visualization tools

Harvest 1.1.2

:: DESCRIPTION

Harvest is a suite of core-genome alignment and visualization tools for quickly analyzing thousands of intraspecific microbial genomes. Harvest includes: Parsnp, a fast core-genome multi-aligner, Gingr, a dynamic visual platform, and harvest-tools, providing both a reference compressed binary archive and format conversion tools.

::DEVELOPER

The University of Maryland Center for Bioinformatics and Computational Biology (CBCB)

:: SCREENSHOTS

Harvest

:: REQUIREMENTS

  • Linux/ MacOsX
  • R
  • BioConductor

:: DOWNLOAD

 Harvest

:: MORE INFORMATION

Citation

Treangen TJ, Ondov BD, Koren S, Phillippy AM.
Rapid Core-Genome Alignment and Visualization for Thousands of Microbial Genomes.”
bioRxiv (2014). doi: http://dx.doi.org/10.1101/007351

Mauve 2.4.0 – Multiple Genome Alignments

Mauve 2.4.0

:: DESCRIPTION

Mauve is a system for efficiently constructing multiple genome alignments in the presence of large-scale evolutionary events such as rearrangement and inversion. Multiple genome alignment provides a basis for research into comparative genomics and the study of evolutionary dynamics on a new scale. Aligning whole genomes is a fundamentally different problem than aligning short sequences.

Mauve has been developed with the idea that a multiple genome aligner should require only modest computational resources. It employs algorithmic techniques that scale well in the amount of sequence being aligned. For example, a pair of Y. pestis genomes can be aligned in under a minute, while a group of 9 divergent Enterobacterial genomes can be aligned in a few hours.

::DEVELOPER

The Darling Lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/ Linux / Mac OsX

:: DOWNLOAD

 Mauve

:: MORE INFORMATION

Citation

Aaron C.E. Darling, Bob Mau, Frederick R. Blatter, and Nicole T. Perna. 2004.
Mauve: multiple alignment of conserved genomic sequence with rearrangements.
Genome Research. 14(7):1394-1403.

BatMis 3.00 – Basic Alignment Tool for Mismatches

BatMis 3.00

:: DESCRIPTION

BatMis is a fast short read aligner allowing up to 10 mismatches

::DEVELOPER

Sung Wing Kin, Ken

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

  BatMis

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Aug 15;28(16):2122-8. doi: 10.1093/bioinformatics/bts339. Epub 2012 Jun 10.
BatMis: a fast algorithm for k-mismatch mapping.
Tennakoon C, Purbojati RW, Sung WK.

PathBLAST – Alignment of Protein Interaction Networks

PathBLAST

:: DESCRIPTION

PathBLAST searches the protein-protein interaction network of the target organism to extract all protein interaction pathways that align with a pathway query.

::DEVELOPER

the Ideker Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W83-8.
PathBLAST: a tool for alignment of protein interaction networks.
Kelley BP, Yuan B, Lewitter F, Sharan R, Stockwell BR, Ideker T.

D2Z 0.1 – Alignment Free Comparison of Regulatory Sequences

D2Z 0.1

:: DESCRIPTION

D2Z is based on comparing the frequencies of all fixed-length words in the two sequences. An important, novel feature of the score is that it is comparable across sequence pairs drawn from arbitrary background distributions.

::DEVELOPER

The Sinha Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

D2Z Source Code

:: MORE INFORMATION

Citation:

A statistical method for alignment-free comparison of regulatory sequences
Miriam R. Kantorovitz,Gene E. Robinson, Saurabh Sinha.
Bioinformatics. 2007 Jul 1;23(13):i249-55.

MP-T 201407 – Membrane Protein Sequence-structure Alignment

MP-T 201407

:: DESCRIPTION

MP-T is a sequence-structure alignment algorithm for membrane proteins. It produces accurate sequence alignments for use in homology modelling. The inputs are a fasta-formatted sequence and an annotated structure file from the iMembrane webserver.

::DEVELOPER

Oxford Protein Informatics Group (OPIG)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  MP-T

:: MORE INFORMATION

Citation

Jamie R. Hill and Charlotte M. Deane
MP-T: improving membrane protein alignment for structure prediction
Bioinformatics (2013) 29 (1): 54-61.

Alignancer 0.6 – Align Unaligned Regions in a HMMer-3 output alignments

Alignancer 0.6

:: DESCRIPTION

Alignancer is a tool for alignment enhancing. It is performing additional alignments on masked sections of hmmalign (HMMER 3.0) multiple alignments. ClustalW (default) or Muscle is being utilized to automatically align all sections which were not covered by a profile HMM and therefore were not aligned. In using additional aligners to complement hmmalign, compulsory loss of information may be avoided keeping the entire alignment for subsequent analyses, e.g. the calculation of phylogenetic trees.

::DEVELOPER

Bioinformatics at AWI

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX / Windows
  • Python

:: DOWNLOAD

 Alignancer

:: MORE INFORMATION