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Multiple Sequence Alignment tool. |
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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. |
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This tool calculates pairwise identity and similarity of a msa using several methods.
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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. |
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An antigen prediction tool that follows the Kolaskar and Tongaonkar (1990) method is available from our antigenic site. |
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A tool that creates a three dimensional representation of variability in HLA molecules.
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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]. |
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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. |
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| 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.
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This server computes binding affinity of peptides to TAP (Transporter Associated with Antigen Processing)
using a Support Vector Machine model. |
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MHCLIG predicts predicts what type of ligands (Peptides, Lipids or None) can bind classical and non-classical MHCI molecules
using machine learning and blast |
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EPISOPT predicts the HLA I-binding profile of epitope peptides and upon them computes their population protection coverage.
Finally, EPISOPT identifies all distinct combinations of epitope peptides reaching a maximum population protection coverage with a minimal number of
peptides |
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This server predicts cleavage sites within a protein generated by the constitutive proteasome or the immunoproteasome using different Ngram models. |
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This server predicts linear B cell epitopes with enhanced immunogeniciy and cross-reactivity with native antigens |
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BepiBlast predicts linear B cell epitopes using a BLAST-based module |
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This server predicts unconventional protein secretion by exosome using random forestss. |
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Modeling & 3D-Structure Analysis |
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This server maps amino acid sequence variability onto 3D structures. |
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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.
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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. |
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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. |
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Sequence Manipulation & Analysis |
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A program which converts the output from a BLAST search into Fasta format. |
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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. |
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This tool calculates pairwise identity and similarity of a msa using several methods.
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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. |
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Provides access to BLAST searches using specialized databases, such as the IMGT/HLA database. |
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An access to PSI-BLAST of NCBI from the Immunomedicine Group web site. |
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This Database searches for peptides that bind to MHC molecules. |
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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. |
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A Database which searches HLA molecules. |
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