BIOINFORMATICS TOOLS
Sequence Alignment ToolsPairwise 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
- CLUSTAL W at EBI
- CLUSTAL W at embnet
- CLUSTAL W at DDBJ
- GeneBee
- T-Coffee at embnet
- T-Cofee at BioASP
- CLUSTAL X:- You can download the program from http://www-igbmc.u-strasbg.fr/BioInfo/ClustalX/Top.html and see the documentation here.
- MultAlin
- MAFFT
- Multiple Sequence Editors:-
Sequence based homology search tools
- BLAST at NCBI (USA) - basic
- BLAST against (un)finished Genomes at NCBI (USA)
- MEGABLAST at NCBI (large set of DNA query sequences)
- MEGABLAST at Harvard (large set of DNA query sequences)
- PSI BLAST at NCBI (USA) - Position Specific Iterated BLAST
- BLAST at EBI (Hinxton, UK)
- BLAST at GenomeNet (Japan)
- BLAST at BCM: Protein searches
- BLAST at PIR-International Protein Sequence Database
- BLAST search in PRODOM
- OWL BLAST Server
- GeneBee Basic BLAST 2.0
- FASTA at EBI (Hinxton, UK)
- FASTA at NPS (France)
- Fasta 3.3
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
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
N-Glycosylation Site Prediction Server
Secondary structure Prediction
AGADIR- An algorithm to predict the helical content of peptides
SSCP- Secondary structural content prediction from amino acid composition
Phylogeny Programs
Joe Felsenstein's Phylogeny programs website
Phylogenetic Analysis Computer Programs
Phylogeny software (Glasgow University)
TreeTop - Phylogenetic Tree prediction
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)
SOAP Stability of aligned positions
FORCON download page (sequence format interconversion for the PC only)
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
