AnDom – Assign Structual Domains to Protein Sequences

AnDom

:: DESCRIPTION

AnDom (Annotation of Domains)is a WEB tool helps to assign structual domains to protein sequences and to classify them according to SCOP.

::DEVELOPER

Bork Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

J Chem Inf Comput Sci. 2002 Mar-Apr;42(2):405-7.
A versatile structural domain analysis server using profile weight matrices.
Schmidt S, Bork P, Dandekar T.

ArchCandy 1.0 – Detect Regions in Protein Sequences that have a potential to form Amyloids

ArchCandy 1.0

:: DESCRIPTION

ArchCandy is able to decode protein sequence motifs that have a potential to form amyloids.

::DEVELOPER

BiSMM – Structural Bioinformatics and Molecular Modeling

:: SCREENSHOTS

ArchCandy

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • Java

:: DOWNLOAD

 ArchCandy

:: MORE INFORMATION

Citation

A structure-based approach to predict predisposition to amyloidosis
Ahmed AB, Znassi N, Chateau MT, Kajava AV
Alzheimers Dement. DOI: 10.1016/j.jalz.2014.06.007

PSAweb – Analysis of Protein Sequence and Multiple Alignment

PSAweb

:: DESCRIPTION

PSAweb is a web server, developed to analyze the amino acid sequence and multiple sequence alignment of proteins. This is a comprehensive on-line Internet tool that allows the rapid visualization of an analysis, by output in GIF format. It assists the user in analyzing and presenting the primary structure of proteins and mutiple alignment of protein sequences

::DEVELOPER

Dr. G P S Raghava

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

Raghava, G. P. S. (2001)
A graphical web server for the analysis of protein sequences and alignment.
Biotech Software and Internet Report 2: 255-8.

PTMPred – Predict Post-transcriptional Modification sites from Protein sequences

PTMPred

:: DESCRIPTION

PTMpred is a tool for predicting post-transcriptional modification sites based on protein sequence.

::DEVELOPER

APORC

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux

:: DOWNLOAD

 PTMpred

:: MORE INFORMATION

Citation

Prediction of posttranslational modification sites from amino acid sequences with kernel methods.
Xu Y, Wang X, Wang Y, Tian Y, Shao X, Wu LY, Deng N.
J Theor Biol. 2014 Mar 7;344:78-87. doi: 10.1016/j.jtbi.2013.11.012.

Prodepth – Predict Residue Depth from Protein Sequences only

Prodepth

:: DESCRIPTION

Prodepth is an online prediction web server for the accurate prediction of residue depth from protein sequences only. It can be used to accurately identify the burial depth status of amino acid residues in a protein.

::DEVELOPER

Akutsu Laboratory , Whisstock Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

PLoS One. 2009 Sep 17;4(9):e7072. doi: 10.1371/journal.pone.0007072.
Prodepth: predict residue depth by support vector regression approach from protein sequences only.
Song J, Tan H, Mahmood K, Law RH, Buckle AM, Webb GI, Akutsu T, Whisstock JC.

MUMmer 4.0.0Beta2 / pymummer 0.11.0 – Alignment of Large-scale DNA & Protein Sequences

MUMmer 4.0.0Beta2/ pymummer 0.11.0

:: DESCRIPTION

MUMmer is a system for rapidly aligning entire genomes, whether in complete or draft form.MUMmer can also align incomplete genomes; it can easily handle the 100s or 1000s of contigs from a shotgun sequencing project, and will align them to another set of contigs or a genome using the NUCmer program included with the system. If the species are too divergent for a DNA sequence alignment to detect similarity, then the PROmer program can generate alignments based upon the six-frame translations of both input sequences.

pymummer is Python3 module for running MUMmer and reading the output

::DEVELOPER

MUMmer team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • GCC / Python

:: DOWNLOAD

MUMmer, pymummer

:: MORE INFORMATION

MUMmer is now an open source project.

Citation:

MUMmer4: A fast and versatile genome alignment system
G. Marçais , A.L. Delcher, A.M. Phillippy, R. Coston, S.L. Salzberg, A. Zimin,
PLoS computational biology (2018), 14(1): e1005944.

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.

PHYSICO 2 – Computation of Properties of Protein Sequences

PHYSICO 2

:: DESCRIPTION

PHYSICO2 is an UNIX based Standalone Procedure for Computation of Physicochemical, Window-dependent and Substitution Based Evolutionary Properties of Protein Sequences along with Automated Block Preparation Tools.

::DEVELOPER

PHYSICO team

:: SCREENSHOTS

Command Line

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 PHYSICO

:: MORE INFORMATION

Citation:

PHYSICO2: an UNIX based standalone procedure for computation of physicochemical, window-dependent and substitution based evolutionary properties of protein sequences along with automated block preparation tool, version 2.
Banerjee S, Gupta PS, Nayek A, Das S, Sur VP, Seth P, Islam RN, Bandyopadhyay AK.
Bioinformation. 2015 Jul 31;11(7):366-8. doi: 10.6026/97320630011366.

REPPER – Detect Regions with Short Gapless REPeats in Protein Sequences

REPPER

:: DESCRIPTION

REPPER (REPeats and their PERiodicities) is an integrated server that detects and analyzes regions with short gapless repeats in protein sequences or alignments. It finds periodicities by Fourier Transform (FTwin) and internal similarity analysis (REPwin). FTwin assigns numerical values to amino acids that reflect certain properties, for instance hydrophobicity, and gives information on corresponding periodicities. REPwin uses self-alignments and displays repeats that reveal significant internal similarities. Both programs use a sliding window to ensure that different periodic regions within the same protein are detected independently. FTwin and REPwin are complemented by secondary structure prediction (PSIPRED) and coiled coil prediction (COILS), making the server a versatile analysis tool for sequences of fibrous proteins.

::DEVELOPER

Söding Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

NO

:: MORE INFORMATION

Citation:

M.Gruber, J. Söding , and A.N.Lupas (2005)
REPPER – repeats and their periodicities in fibrous proteins
Nucl. Acids Res., 33(2), W239-43

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.