GlycoPP 1.0 – Prediction of Glycosites in Prokaryotic Protein Sequences

GlycoPP 1.0

:: DESCRIPTION

GlycoPP is a webserver for predicting potential N-and O-glycosites in prokaryotic protein sequence(s), where N-glycosite is an Asn residue and O-glycosite could be a serine or threonine residue having a glycan attached covalently and enzymatically at amide or hydroxyl group respectively.

::DEVELOPER

GlycoPP team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

PLoS One. 2012;7(7):e40155. doi: 10.1371/journal.pone.0040155. Epub 2012 Jul 9.
GlycoPP: a webserver for prediction of N- and O-glycosites in prokaryotic protein sequences.
Chauhan JS1, Bhat AH, Raghava GP, Rao A.

VLASPD – Discovering Variable-Length Patterns in Protein Sequences for PPI Prediction

VLASPD

:: DESCRIPTION

VLASPD considers variable-length segments in protein sequences for protein-protein Interaction prediction

::DEVELOPER

Allen, Lun Hu

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux
  • JRE

:: DOWNLOAD

 VLASPD

:: MORE INFORMATION

Citation

IEEE Trans Nanobioscience. 2015 May 21
Discovering Variable-Length Patterns in Protein Sequences for Protein-Protein Interaction Prediction.
Hu L, Chan K.

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.

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

Waggawagga team

:: 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.

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 , Whisstock 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.

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

JCI BioInfo 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.

UFO – Functional Profiling of Whole Genome Protein Sequences

UFO

:: DESCRIPTION

UFO (ultra-fast functional profiling) is a web server for ultra-fast functional profiling of whole genome protein sequences.

::DEVELOPER

Department of Bioinformatics ,  University of Göttingen

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

BMC Genomics. 2009 Sep 2;10:409. doi: 10.1186/1471-2164-10-409.
UFO: a web server for ultra-fast functional profiling of whole genome protein sequences.
Meinicke P.

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.

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.

Swat – Aligning DNA/RNA sequences and Protein sequences

Swat

:: DESCRIPTION

Swat is a java commandline software based on dynamic programming to calculate optimal local alignments of DNA/RNA sequences and protein sequences.

::DEVELOPER

Medical Systems Biology, University of Ulm

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows /MacOsX
  • Java

:: DOWNLOAD

 Swat

:: MORE INFORMATION