BIOINFORMATICS TOOLS

Sequence Alignment Tools

Pairwise Sequence Alignment

  • Dot Matrix Plot:-Dot or matrix plots provide an easy and powerful means of sequence analysis, useful for searching out regions of similarity in two sequences and repeats within a single sequence
  • ALIGN:-This tool at EBI is very frequently used for both local and global alignments of sequences.
  • LALIGN:-Alignments of 2 sequences
  • Dotlet:-a Java applet for dotmatrix sequence comparisons
  • BLAST 2 Sequences:- This tool produces the alignment of two given sequences using BLAST engine for local alignment.
  • SIM:-Alignment tool for protein sequences at Expasy.
  • WISE:-Align protein and genomic Sequences at Pasteur.
  • JAligner:-Open source Java Implementation of Smith Watermann algorithm.

Multiple Sequence Alignment

Sequence based homology search tools

 

Protein Sequence Alignment Tools

General Protein Information

Hydrophobicity Plots:-They are useful in predicting membrane-spanning domains, potential antigenic sites and regions that are likely exposed on the protein's surface.

AACompSim is a tool which allows the comparison of the amino acid composition of a Swiss-Prot entry with all other Swiss-Prot entries so as to find the proteins whose amino acid compositions are closest to that of the selected entry

Genetic Code Viewer

PeptideMass Calculate masses of peptides and their post-translational modifications for a UniProtKB/Swiss-Prot or UniProtKB/TrEMBL entry or for a user sequence

CUTTER is tool to generate and analyze proteolytic cleavage.

 

Motifs/Pattern Searching

NPS@ : PATTINPROT search

PROSITE

PRATT

PatScan

PatternFind

Motif Explorer

N-Glycosylation Site Prediction Server

BNL motif searching

MOTIFS in SwissProt at IBCP

PRINTS

BLOCKS

PRODOM

SBASE

MOTIF at GenomeNet (Japan)

 

Secondary structure Prediction

AGADIR- An algorithm to predict the helical content of peptides

SSCP- Secondary structural content prediction from amino acid composition

GOR

PREDATOR

PredictProtein

 

Phylogeny Programs

Joe Felsenstein's Phylogeny programs website

Phylogenetic Analysis Computer Programs

Phylogeny software (Glasgow University)

TreeTop - Phylogenetic Tree prediction

CMBI CLUSTAL W

Puzzle: Tree reconstruction for sequences by quartet puzzling and maximum likelihood (Strimmer, von Haeseler)

MacClade Home Page

PAUP

Morkov Chain Monte Carlo - phylogeteic analysis (USA)

Morkov Chain Monte Carlo - phylogeteic analysis (UK)

Morkov Chain Monte Carlo - Molecular clock

TREECON download page (demo version)

Phylogeny server at Pasteur

SOAP Stability of aligned positions

TreeEdit

FORCON download page (sequence format interconversion for the PC only)

Mesquite

 

Protein Structure Prediction

Comparative Modelling

SWISS-MODEL - An automated knowledge-based protein modelling server

3Djigsaw - Three-dimensional models for proteins based on homologues of known structure

Geno3d - Automatic modelling of protein three-dimensional structure

SDSC1 - Protein Structure Homology Modeling Server

CPHmodels - Automated neural-network based protein modelling server

Threading

3D-PSSM - Protein fold recognition using 1D and 3D sequence profiles coupled with secondary structure information

LOOPP - Sequence to sequence, sequence to structure, and structure to structure alignment

Ab initio

Rosetta Server -Rosetta Server predicts the structure of proteins from the sequence : secondary, local, supersecondary, and tertiary.

 

Molecular Visualization Tools

Rasmol

Swiss PDB Viewer

MolMol

VMD

Cn3d

Pymol

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