TargetFreeze – Protein Sequence-based AFP predictor

TargetFreeze

:: DESCRIPTION

TargetFreeze is a supplement method to existing AFPs (Antifreeze proteins) predictors and will have potential applications in AFPs-related biotechnology fields.

::DEVELOPER

Pattern Recognition and Bioinformatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

J Membr Biol. 2015 Jun 10.
TargetFreeze: Identifying Antifreeze Proteins via a Combination of Weights using Sequence Evolutionary Information and Pseudo Amino Acid Composition.
He X1, Han K, Hu J, Yan H, Yang JY, Shen HB, Yu DJ.

AlignBucket – Identify Optimized Subsets of Protein Sequences for Alignment

AlignBucket

:: DESCRIPTION

AlignBucket is a software for splitting a fasta file into smaller pieces suitable for alignment with BLAST. The constraint used to optimize the result is the required minimum alignment coverage.

::DEVELOPER

Giuseppe Profiti , Piero Fariselli

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • g++

:: DOWNLOAD

 AlignBucket

:: MORE INFORMATION

Citation

Bioinformatics. 2015 Jul 30. pii: btv451.
AlignBucket: a tool to speed up ‘all-against-all’ protein sequence alignments optimizing length constraints.
Profiti G, Fariselli P, Casadio R

PSIVER – Prediction of Protein-protein Interaction Sites in Protein Sequences

PSIVER

:: DESCRIPTION

PSIVER (Protein-protein interaction SItes prediction seVER)  is a server for the prediction of protein-protein interaction sites in protein sequences.

::DEVELOPER

the Mizuguchi Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Server

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Bioinformatics. 2010 Aug 1;26(15):1841-8. doi: 10.1093/bioinformatics/btq302. Epub 2010 Jun 6.
Applying the Naive Bayes classifier with kernel density estimation to the prediction of protein-protein interaction sites.
Murakami Y, Mizuguchi K.

UProC 1.2.0 – Tools for Ultra-fast Protein Sequence Classification

UProC 1.2.0

:: DESCRIPTION

The UProC (ultrafast protein classification) toolbox implements a novel algorithm (“Mosaic Matching”) for large-scale sequence analysis and is now available in terms of an open source C library. UProC is up to three orders of magnitude faster than profile-based methods and achieved up to 80% higher sensitivity on unassembled short reads (100 bp) from simulated metagenomes. UProC does not depend on a multiple alignment of family-specific sequences. Therefore, in addition to the protein domain classfication according to the Pfam database, UProC can, in principle, also provide the detection of KEGG Orthologs

::DEVELOPER

Dr. Peter Meinicke

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • C++ Compiler

:: DOWNLOAD

 UProC

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Dec 23. pii: btu843.
UProC: tools for ultra-fast protein domain classification.
Meinicke P

PISCES 20210711 – Protein Sequence Culling Server

PISCES 20210711

:: DESCRIPTION

PISCES (Protein Sequence Culling Server) is a database server for producing lists of sequences from the Protein Data Bank (PDB) using a number of entry- and chain-specific criteria and mutual sequence identity.

::DEVELOPER

Dunbrack Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Mac /  Linux
  • Perl

:: DOWNLOAD

PISCES

:: MORE INFORMATION

Citation

Guoli Wang and Roland L. Dunbrack Jr.
PISCES: a protein sequence culling server“,
Bioinformatics 19:1589-1591, 2003.

C-HMM 1.0 – Program to Identify Remote Homologues from Protein Sequence Database

C-HMM 1.0

:: DESCRIPTION

C-HMM is a software to detect remote/distant homologues from protein sequence databases. It is based on HMMs(Hidden Markov Models) for identifying the deep evolutionary relationships of protein sequences.

::DEVELOPER

C-HMM team

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux / MacOsX
  • Java
  • HMMER3

:: DOWNLOAD

 C-HMM

:: MORE INFORMATION

Citation

Rapid and Enhanced Remote Homology Detection by Cascacading Hidden Markov Model Searches in Sequence Space.
Kaushik S, Nair AG, Mutt E, Prasanna H, Sowdhamini R.
Bioinformatics. 2015 Oct 10. pii: btv538.

Pse-in-One 1.0.6 – Generating various modes of Pseudo Components of DNA, RNA and Protein Sequences

Pse-in-One 1.0.6

:: DESCRIPTION

Pse-in-One is a web server for generating various modes of pseudo components of DNA, RNA and protein sequences

::DEVELOPER

Liu Lab, Harbin Institute of Technology Shenzhen Graduate School.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Python

:: DOWNLOAD

 Pse-in-One

:: MORE INFORMATION

Citation

Pse-in-One: a web server for generating various modes of pseudo components of DNA, RNA, and protein sequences.
Liu B, Liu F, Wang X, Chen J, Fang L, Chou KC.
Nucleic Acids Res. 2015 Jul 1;43(W1):W65-71. doi: 10.1093/nar/gkv458.

CS-PSeq-Gen 1.0 – Simulation of Protein Sequences under Constraints

CS-PSeq-Gen 1.0

:: DESCRIPTION

CS-PSeq-Gen is a program derived from PSeq-Gen, a program developed by Nick C. Grassly and Andrew Rambaut, designed to simulate the evolution of protein sequences along evolutionary trees. CS-PSeq-Gen modifications are related to the aim of simulating the evolution of protein sequences under the constraints of the information of a particular reconstructed phylogeny: the “root sequence” that initiates the simulation, or the rate heterogeneity among sites are specific on each particular protein family. CS-Pseq-Gen will allow simulations to take such information into account. As well, exploring the evolution of one protein family and testing hypotheses makes often it necessary to have some control on the variability of the parameters. CS-PSeq-Gen will allow some control on the simulated tree / branch lengths around an average value. Finally, a particular category of applications for such simulations is the search for the significant co-evolution of sites. CS-PSeq-Gen offers some facilities to generate sequences under such hypotheses, and propose a basic scheme for their detection, that can be easily adapted by programmers.

::DEVELOPER

P. Tufféry  (tuffery@ebgm.jussieu.fr )

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 CS-PSeq-Gen

:: MORE INFORMATION

Citation

Tufféry, P.
CS-PSeq-Gen: Simulating the evolution of protein sequence under constraints
Bioinformatics, Volume 18, Number 7, July 2002 , pp. 1015-1016(2)

tantan 22 – Find Cryptic Repeats in DNA, RNA, and Protein Sequences.

tantan 22

:: DESCRIPTION

tantan is a tool to mask simple regions (low complexity and short-period tandem repeats) in DNA, RNA, and protein sequences.The aim of tantan is to prevent false predictions when searching for homologous regions between two sequences. Simple repeats often align strongly to each other, causing false homology predictions.

::DEVELOPER

Martin C. Frith

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ compiler

:: DOWNLOAD

 tantan

:: MORE INFORMATION

Citation

MC Frith,
A new repeat-masking method enables specific detection of homologous sequences,
Nucleic Acids Research 2011 39(4):e23.

AMS 4.0-1.5 – Consensus Prediction of Post-translational Modifications in Protein Sequences

AMS 4.0-1.5

:: DESCRIPTION

AMS (AutoMotif Service) predicts the wide selection of 88 different types of the single amino acid post-translational modifications (PTM) in protein sequences.

::DEVELOPER

AMS team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C Compiler

:: DOWNLOAD

 AMS

:: MORE INFORMATION

Citation

Amino Acids. 2012 Aug;43(2):573-82. doi: 10.1007/s00726-012-1290-2.
AMS 4.0: consensus prediction of post-translational modifications in protein sequences.
Plewczynski D, Basu S, Saha I.