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TOOLS
 
  Alignment Analysis
  Databases
  Computational Immunology
  Modeling & 3D-structure     Analysis
  Sequence Manipulation &     Analysis
  Similarity Searches
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 Tools 
  Alignment Analysis

Tool
Description
CLUSTALW
Multiple Sequence Alignment tool.
ENDscript 1.0
An interface grouping seven programs: BLAST; MULTALIN/ CLUSTALW; DSSP; CNS; ESPript; BOBSCRIPT/ MOLSCRIPT; PHYLODENDRON. Aims to produce from a single PDB file, three PostScript figures containing most required sequence and structure information on a protein. Just upload your PDB and hit the RUN button.
Local version outdated. You will be redirected to main site.
ESPript 2.0
Generate a pretty PostScript output from aligned sequences. Obtain coloring and residue grouping in the output from a similarity score calculated following several optinals algorithms. Take a PDB file with the 3D-coordinates of the first sequence in the alignment, in which case the ouput is enhanced with the secondary structure, solvent accessibility, and hydropathy.
Click here for an updated version of the server.
Seqlogos
SeqLogos generate sequences logos from amino acid sequence alignment. Sequences logos are useful tools to visualyze sequence pattenrs and represent a more informative alternative to consesus sequence.
SIAS
This tool calculates pairwise identity and similarity of a msa using several methods.
PVS
A server which calculates the variability of multiple sequence alignments using the Shannon entropy (H) function, the Simpson entropy function and the Wu-Kabat entropy function.

  Computational Immunology

Tool
Description
Antigenic Peptide Prediction
An antigen prediction tool that follows the Kolaskar and Tongaonkar (1990) method is available from our antigenic site.
HLAV3D
A tool that creates a three dimensional representation of variability in HLA molecules.
PEPVAC
A tool designed to aid in the development of multi-epitope vaccines against pathogenic organisms based on genome-wide predictions of promiscous MHCI-restricted epitopes [Restricted Access].
PVS
A server which calculates the variability of multiple sequence alignments using the Shannon entropy (H) function, the Simpson entropy function and the Wu-Kabat entropy function.
Rankpep
Predicts MHC binding peptides from an input protein based on their similarity to a set of peptides known to bind to a given MHC molecule. Similarity is scored using Position Specific Scoring Matrixes (PSSM) derived from the aligned peptides known to bind to that MHC molecule.
TAPREG
This server computes binding affinity of peptides to TAP (Transporter Associated with Antigen Processing) using a Support Vector Machine model.
PCPS
This server predicts cleavage sites within a protein generated by the constitutive proteasome or the immunoproteasome using different Ngram models.
MHCLIG
This server predicts whether MHC I and related molecules can bind any ligand at all, and if so, the chemical nature of the ligad: Peptides, Modified Peptides, Lipids or vitamin B metabolites
EPISOPT
EPISOFT predicts epitope HLA I binding profiles and computes population protection (PPC). It also identifies minimal sets of epitopes that reach a target PPC for 5 distinct user-selected ethnic groups.

  Modeling & 3D-Structure Analysis

Tool
Description
H2PDB
This server maps amino acid sequence variability onto 3D structures.
ENDscript 1.0
An interface grouping seven programs: BLAST; MULTALIN/ CLUSTALW; DSSP; CNS; ESPript; BOBSCRIPT/ MOLSCRIPT; PHYLODENDRON. Aims to produce from a single PDB file, three PostScript figures containing most required sequence and structure information on a protein. Just upload your PDB and hit the RUN button.
Local version is outdated. You will redirected to main the site.
MSAT
Identifying solvent exposed hydrophobic residues from within a protein sequence, and compares them with those of closely related sequences, making it possible to select the optimal residues to target for site-directed mutagenesis.
PVS
A server which calculates the variability of multiple sequence alignments using the Shannon entropy (H) function, the Simpson entropy function and the Wu-Kabat entropy function.

  Sequence Manipulation & Analysis

Tool
Description
BLAST2FASTA
A program which converts the output from a BLAST search into Fasta format.
DACHIS
A program to recognize and classify histons
Methylator
Prediction of DNA methylation in CpG dinucleotides.
E-northern
Retrieves expression data from protein/DNA sequence query using the annotation of UniGene EST clusters.
EMBOSS
European Molecular Biology Open Software Suite, a suite of free software tools for sequence analysis. There are a wide variety of programs that make up the suite, ranging in application from database searching to presentation of sequence data.
SIAS
This tool calculates pairwise identity and similarity of a msa using several methods.
SMS - The Sequence Manipulation Suite
A collection of web-based programs for analyzing and formatting DNA and protein sequences. The output of each program is a set of HTML commands, which is rendered by web browser as a standard web page. The results can be printed, saved, and edited using an HTML editor or a text editor.

  Similarity Searches

Tool
Description
NCBI-Blast
Provides access to BLAST searches using specialized databases, such as the IMGT/HLA database.
PSI-Blast
An access to PSI-BLAST of NCBI from the Immunomedicine Group web site.

  Databases

Tool
Description
EPIMHC Database
This Database searches for peptides that bind to MHC molecules.
EPIPOX Database
This database contains results for an analysis of poxvirus ortholog proteins across several viral strains, and sequences from those proteins that are predicted by Rankpep analysis to bind to alleles.
HLA Database
A Database which searches HLA molecules.


All Tools
Antigenic Peptide Prediction
BLAST2FASTA
DACHIS
EMBOSS
E-Northern
EPIMHC Database
EPIPOX Database
EPISOPT
H2PDB
HLA Database
HLAV3D
MHCLIG
Methylator
MSAT
NCBI-Blast
PCPS
PEPVAC
PSI-Blast
PVS
Rankpep
SeqLogo
SIAS
SMS
TAPREG
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