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

 

GASOLINE 2.0 – Optimal Local multiple Alignment of Interaction NEtworks

GASOLINE 2.0

:: DESCRIPTION

GASOLINE (Greedy and Stochastic Algorithm for Optimal Local alignment of Interaction Networks) is an algorithm for multiple local network alignment based on statistical iterative sampling in connection to a greedy strategy. GASOLINE can produce biologically significant alignments in reasonable running time, even for very large input instances.

::DEVELOPER

Giovanni Micale

:: SCREENSHOTS

GASOLINE

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • CytoScape
  • JRE

:: DOWNLOAD

 GASOLINE

:: MORE INFORMATION

Citation:

Micale G, Pulvirenti A, Giugno R, Ferro A (2014)
GASOLINE: a Greedy And Stochastic algorithm for Optimal Local multiple alignment of Interaction NEtworks.
PLoS ONE 9(6): e98750. doi: 10.1371/journal.pone.0098750

PROPOSAL – PROtein Comparison through Probabilistic Optimal Structure local ALignment

PROPOSAL

:: DESCRIPTION

PROPOSAL is a Gibbs sampling algorithm for multiple local alignment of 3D protein structures. PROPOSAL can produce biologically significant alignments in reasonable running time, even for large input instances.

::DEVELOPER

Giovanni Micale

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • Java

:: DOWNLOAD

  PROPOSAL

:: MORE INFORMATION

Citation:

Proteins comparison through probabilistic optimal structure local alignment.
Micale G, Pulvirenti A, Giugno R, Ferro A.
Front Genet. 2014 Sep 2;5:302. doi: 10.3389/fgene.2014.00302.

PINALOG 1.0 – Protein Interaction Network Alignment

PINALOG 1.0

:: DESCRIPTION

PINALOG is a protein-protein interaction(PPI) network alignment method aiming to map similar parts of PPI networks in terms of protein similarity (by both sequence and function) and the local network similarity. PINALOG incorporates not only sequence similarity and topological similarity of proteins in the equivalencing process but also uses the function similarity of protein pairs.

::DEVELOPER

Structural Bioinformatics Group, Imperial College

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux

:: DOWNLOAD

 PINALOG

:: MORE INFORMATION

Citation

Bioinformatics. 2012 May 1;28(9):1239-45. doi: 10.1093/bioinformatics/bts119. Epub 2012 Mar 13.
PINALOG: a novel approach to align protein interaction networks–implications for complex detection and function prediction.
Phan HT, Sternberg MJ.

lara 1.3.2a – Sequence-structure Alignment of RNA Sequences

lara 1.3.2a

:: DESCRIPTION

lara (“lagrangian relaxed structural alignment”) is a tool for the sequence-structure alignment of RNA sequences.

::DEVELOPER

Life Sciences Group, Centrum Wiskunde & Informatica

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • T-Coffee

:: DOWNLOAD

 lara

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2007 Jul 27;8:271.
Accurate multiple sequence-structure alignment of RNA sequences using combinatorial optimization.
Bauer M1, Klau GW, Reinert K.

PAUL 2.0 – Protein Distance Matrix Alignment

PAUL 2.0

:: DESCRIPTION

PAUL (Protein Alignment Using Lagrangian relaxation) is a tool for the computation of protein structure alignments based on sparse protein distance matrices

::DEVELOPER

Life Sciences Group, Centrum Wiskunde & Informatica

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • T-Coffee

:: DOWNLOAD

 PAUL

:: MORE INFORMATION

Citation

Bioinformatics. 2010 Sep 15;26(18):2273-80. doi: 10.1093/bioinformatics/btq420. Epub 2010 Jul 17.
Towards optimal alignment of protein structure distance matrices.
Wohlers I1, Domingues FS, Klau GW.