ANNIE – Protein Sequence Annotation and Interpretation Environment

ANNIE

:: DESCRIPTION

ANNIE is a comprehensive de novo protein annotation system that integrates a large number of indispensable algorithms used in everyday sequence analytic work.

::DEVELOPER

Bioinformatics Institute (BII), Singapore.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2009 Jul;37(Web Server issue):W435-40. doi: 10.1093/nar/gkp254. Epub 2009 Apr 23.
ANNIE: integrated de novo protein sequence annotation.
Ooi HS, Kwo CY, Wildpaner M, Sirota FL, Eisenhaber B, Maurer-Stroh S, Wong WC, Schleiffer A, Eisenhaber F, Schneider G

BioSeq-Analysis 2.0 / BioSeq-BLM 1.0 – Analyzing DNA, RNA, and Protein Sequences based on Biological Language Models

 BioSeq-Analysis 2.0 / BioSeq-BLM 1.0

:: DESCRIPTION

BioSeq-Analysis is an platform for analyzing DNA, RNA, and protein sequences at sequence level and residue level based on machine learning approaches

BioSeq-BLM is a platform for analyzing DNA, RNA, and protein sequences based on biological language models

::DEVELOPER

Liu Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux

:: DOWNLOAD

BioSeq-Analysis / BioSeq-BLM

:: MORE INFORMATION

Citation

Liu B, Gao X, Zhang H.
BioSeq-Analysis2.0: an updated platform for analyzing DNA, RNA and protein sequences at sequence level and residue level based on machine learning approaches.
Nucleic Acids Res. 2019 Nov 18;47(20):e127. doi: 10.1093/nar/gkz740. PMID: 31504851; PMCID: PMC6847461.

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.

RSARF – Prediction of Solvent Accessibility from Protein Sequence using Random Forest Method

RSARF

:: DESCRIPTION

RSARF is a random forest method to predict residue accessible surface area from protein sequence information.

::DEVELOPER

RSARF team

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Windows/ Linux
  • R

:: DOWNLOAD

 RSARF

:: MORE INFORMATION

Citation

Protein Pept Lett. 2012 Jan;19(1):50-6.
RSARF: prediction of residue solvent accessibility from protein sequence using random forest method.
Pugalenthi G1, Kandaswamy KK, Chou KC, Vivekanandan S, Kolatkar P.

HemeBIND / HemeBIND+ – Heme Binding Residue Prediction from Protein Sequence and Structure

HemeBIND / HemeBIND+

:: DESCRIPTION

HemeBIND is an efficient algorithm for predicting heme binding residues by integrating structural and sequence information.

HemeBIND+ predicts heme-binding residues based on the hybrid machine learning (with structural and sequence features) and template-based approaches.

::DEVELOPER

Machine Learning and Evolution Laboratory (MLEG)

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Web Browser
:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

BMC Bioinformatics. 2011 May 26;12:207. doi: 10.1186/1471-2105-12-207.
HemeBIND: a novel method for heme binding residue prediction by combining structural and sequence information.
Liu R1, Hu J.

CAPS 2.0 – Coevolution Analysis using Protein Sequences

CAPS 2.0

:: DESCRIPTION

CAPS (Coevolution Analysis using Protein Sequences) is a PERL based software that identifies co-evolution between amino acid sites. Blosum-corrected amino acid distances are used to identify amino acid co-variation. The phylogenetic sequence relationships are used to remove the phylogenetic and stochastic dependencies between sites. The 3D protein structure is used to identify the nature of the dependencies between co-evolving amino acid sites.

CAPS Online Version

::DEVELOPER

Dr Mario Fares 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Perl

:: DOWNLOAD

 CAPS

:: MORE INFORMATION

Citation

CAPS: coevolution analysis using protein sequences.
Fares MA, McNally D.
Bioinformatics. 2006 Nov 15;22(22):2821-2. Epub 2006 Sep 27.

ModView 0.903 – Visualization of Multiple Protein Sequences & Structures

ModView 0.903

:: DESCRIPTION

ModView is a program to visualize and analyze multiple biomolecule structures and/or sequence alignments. As a Netscape plug-in , it can be embed into Web pages and controlled by JavaScript objects on the page. It has wide range of tools to manipulate and analyze sequences and structures by interactive control.

::DEVELOPER

Andrej Sali

:: SCREENSHOTS

:: REQUIREMENTS

  • Netscape 4.xx

:: DOWNLOAD

ModView

:: MORE INFORMATION

Citation:

Bioinformatics. 2003 Jan;19(1):165-6.
ModView, visualization of multiple protein sequences and structures.
Ilyin VA, Pieper U, Stuart AC, Marti-Renom MA, McMahan L, Sali A.

protr 1.6-2 / ProtrWeb – Generating Various Numerical Representation Schemes of Protein Sequence

protr 1.6-2 / ProtrWeb

:: DESCRIPTION

protr is a comprehensive R package for generating various numerical representation schemes of proteins and peptides from amino acid sequence.

ProtrWeb is an online version

::DEVELOPER

Nan Xiao

:: SCREENSHOTS

N/a

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • R

:: DOWNLOAD

 protr

:: MORE INFORMATION

Citation

protr/ProtrWeb: R package and web server for generating various numerical representation schemes of protein sequences.
Xiao N, Cao DS, Zhu MF, Xu QS.
Bioinformatics. 2015 Jan 24. pii: btv042

LCR-eXXXplorer – Search, Visualize and Share data for low Complexity Regions in Protein sequence

LCR-eXXXplorer

:: DESCRIPTION

LCR-eXXXplorer is a web-service designed to assist biologists in displaying, searching and sharing Low Complexity Regions (LCRs) contained within protein sequences.

::DEVELOPER

LCR-eXXXplorer team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

LCR-eXXXplorer: a web platform to search, visualize and share data for low complexity regions in protein sequences.
Kirmitzoglou I, Promponas VJ.
Bioinformatics. 2015 Feb 20. pii: btv115.

RBRIdent – Identification of RNA-binding Residues in Proteins from primary Sequences

RBRIdent

:: DESCRIPTION

RBRIdent is an algorithm for improved identification of RNA-binding residues in proteins from primary sequences.

::DEVELOPER

Dr. Gong’s Lab

:: SCREENSHOTS

N/a

:: REQUIREMENTS

  • Linux
  • R
  • C++ Compiler

:: DOWNLOAD

  RBRIdent

:: MORE INFORMATION

Citation

Proteins. 2015 Apr 3. doi: 10.1002/prot.24806.
RBRIdent: An algorithm for improved identification of RNA-binding residues in proteins from primary sequences.
Xiong D1, Zeng J, Gong H.