MPAlign-editor 3.0.0 – Graphical Tool for DNA and Protein Sequences and Alignments

MPAlign-editor 3.0.0

:: DESCRIPTION

MPAlign-editor is a graphical tool for DNA and Protein sequences and alignments.

::DEVELOPER

Frederico Arnoldi (fgcarnoldi@gmail.com)

:: SCREENSHOTS

mpalign-editor

:: REQUIREMENTS

  • Linux / Windows / Mac OsX
  • Python

:: DOWNLOAD

 MPAlign-editor

:: MORE INFORMATION

Citation

MPAlign editor: uma ferramenta gráfica e intuitiva para alinhamentos moleculares.
Frederico GC Arnoldi 2005
Proceedings of II Workshop TIDIA—FAPESP

TREMOLO-HCA – Analysis of Distant Relationships between Protein Sequences

TREMOLO-HCA

:: DESCRIPTION

TREMOLO-HCA (Traveling into REmote hoMOLOgy with HCA) is a tool for the analysis of distant relationships between protein sequences. It allows an easier interpretation of the PSI-BLAST results by adding information on the domain architecture (deduced from the CDD database) of proteins with which the query sequence is aligned, as well on the conservation of hydrophobic amino acids that may be critical for the fold. HCA plots of the aligned sequences can also be displayed, allowing their comparison at the 2D level.

::DEVELOPER

Isabelle Callebaut

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • python
  • BioPython
  • blast

:: DOWNLOAD

 TREMOLO-HCA

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Jul 15;29(14):1726-33. doi: 10.1093/bioinformatics/btt271. Epub 2013 May 14.
Identification of hidden relationships from the coupling of hydrophobic cluster analysis and domain architecture information.
Faure G1, Callebaut I.

TANGLE – Protein Backbone Torsion Angle Prediction from Primary Sequences

TANGLE

:: DESCRIPTION

TANGLE (Torsion ANGLE) predictor works by integrating multiple local sequence profiles in combination with global sequence features within a two-level SVR learning framework. Input features include evolutionary profiles in the form of position-specific scoring matrices (PSSMs), predicted secondary structure, solvent accessibility and native disorder information. Moreover, other global sequence information such as sequence length and sequence weight were also used as input to TANGLE.

::DEVELOPER

Akutsu Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

PLoS One. 2012;7(2):e30361. doi: 10.1371/journal.pone.0030361.
TANGLE: two-level support vector regression approach for protein backbone torsion angle prediction from primary sequences.
Song J, Tan H, Wang M, Webb GI, Akutsu T.

Waggawagga – Coiled-coil and Single-Alpha-Helix prediction for Protein Sequences

Waggawagga

:: DESCRIPTION

Waggawagga is a web-based tool for the comparative visualization of coiled-coil predictions and the detection of stable single α-helices (SAH domains).

::DEVELOPER

kollmar_group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Waggawagga: Comparative visualization of coiled-coil predictions and detection of stable single α-helices (SAH domains).
Simm D, Hatje K, Kollmar M.
Bioinformatics. 2014 Oct 22. pii: btu700.

Maxflow 0.1.1 – Alignment of Protein Sequences based on Pairwise Consistency

Maxflow 0.1.1

:: DESCRIPTION

MaxFlow, a greedy algorithm, using a novel consistency score to estimate the relative likelihood of alternative paths of transitive alignment. In contrast to traditional profile models of amino acid preferences, MaxFlow models the probability that two positions are structurally equivalent and retains high information content across large distances in sequence space. Thus, MaxFlow is able to identify sparse and narrow active-site sequence signatures which are embedded in high-entropy sequence segments in the structure based multiple alignment of large diverse enzyme superfamilies.

::DEVELOPER

Liisa Holm’s Bioinformatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 Maxflow

:: MORE INFORMATION

Citation:

J Comput Biol. 2004;11(5):843-57.
Accurate detection of very sparse sequence motifs.
Heger A, Lappe M, Holm L.

PPS – Find Palindromes in all Protein Sequences

PPS

:: DESCRIPTION

PPS (Palindromes in Protein Sequences) is a computing engine  identify palindrome and SAARs in the protein sequences available in various databases.

::DEVELOPER

PPS team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Bioinformation. 2014 Jan 29;10(1):48-51. doi: 10.6026/97320630010048. eCollection 2014.
PPS: A computing engine to find Palindromes in all Protein sequences.
Ahmed Z, Gurusaran M, Narayana P, Kumar KS, Mohanapriya J, Vaishnavi MK, Sekar K.

Cube – Comparative Analysis of Protein Sequences

Cube

:: DESCRIPTION

Cube finds both overall conserved and sub-family specific residues for the user-uploaded sets of protein sequences

::DEVELOPER

Dogmatic Central

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • C compiler

:: DOWNLOAD

 Cube

:: MORE INFORMATION

Citation:

PLoS One. 2013 Nov 20;8(11):e79480. doi: 10.1371/journal.pone.0079480.
Cube – an online tool for comparison and contrasting of protein sequences.
Zhang ZH, Khoo AA, Mihalek I.

SCPS 0.9.8 – Spectral Clustering of Protein Sequences

SCPS 0.9.8

:: DESCRIPTION

SCPS is an efficient, user-friendly, scalable and multi-platform implementation of a spectral clustering method for clustering homologous proteins. SCPS also implements connected component analysis and hierarchical clustering, integrates TribeMCL and interfaces with external tools such as Cytoscape and NCBI BLAST.

::DEVELOPER

Paccanaro Lab

:: SCREENSHOTS

SCPS

::REQUIREMENTS

  • Windows/ Linux / MacOsX

:: DOWNLOAD

 SCPS

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2010 Mar 9;11:120. doi: 10.1186/1471-2105-11-120.
SCPS: a fast implementation of a spectral method for detecting protein families on a genome-wide scale.
Nepusz T1, Sasidharan R, Paccanaro A.

2D-MH – Generating Graphic Representation of Protein Sequences

2D-MH

:: DESCRIPTION

2D-MH is a web-server for generating graphic representation of protein sequences based on the physicochemical properties of their constituent amino acids.

::DEVELOPER

Xiao Lab

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

2D-MH: A web-server for generating graphic representation of protein sequences based on the physicochemical properties of their constituent amino acids.
Wu ZC, Xiao X, Chou KC.
J Theor Biol. 2010 Nov 7;267(1):29-34. doi: 10.1016/j.jtbi.2010.08.007.