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 Tools 
  Immunology

Tool Description
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.
Sequence Variability and Consensus Plots Uses the Shannon Entropy function (H) to evaluate the sequence variability within a multiple sequence alignment. The sequence variability is then plotted against a selected sequence, and the regions with a variability under a given value sorted.
Antigenic Peptide Prediction An antigen prediction tool that follows the Kolaskar and Tongaonkar (1990) method is available from our antigenic site.
E-Northern Tool Retrieves expression data from protein/DNA sequence query using the annotation of UniGene EST clusters.
PEPVAC: Vaccine Design using Promiscuous MHC-I Restricted Peptides. 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].

  Sequence Searches

Tool Description
NCBI-BLAST Provides access to BLAST searches using specialized databases, such as the IMGT/HLA database.
PSI-BLAST: Position Specific Iterative BLAST An access to PSI-BLAST of NCBI from MIF web site.
GenScan Identifies genes from genomic sequences. Gene exons and introns are predicted and the encoded protein sequence is returned.
SeqLogo SeqLogo 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.
Dachis It is a novel method for delination & classification of histones. It is based on Amino acid Composition. The method has been developed using SVM. The method is able to discrmate between histone & non-histones with more than 99% accuracy. The method is further able to classify histone with 98% accuracy.
Methylator Methylator accepts a single nucleotide sequence. After the analysis, the results provide the summary of the summated sequence in term of length, selected threshold and time of prediction. The methylated cytosines are shown in bolder and red color as compare to rest of the cytosines.

  Sequence Manipulation

Tool Description
Sequence Manipulation Suite (SMS) 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.
BLAST2FASTA A program which converts the output from a BLAST search into Fasta format.
SVA A server which calculates the variability from multiple sequence alignment using the Shannon entropy (H) function.

  DNA & Protein Analysis

Tool Description
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.

  Structure Analysis

Tool Description
H2PDB - Map Sequence variability (H) onto a 3D structure This server maps amino acid sequence variability onto 3D structures.
Modeling and Solvent Accessibility Tool 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.
ESPript: Easy Sequencing in Postscript 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 aligment, in which case the ouput is enhanced with the secondary structure, solvent accessibility, and hydropathy.
ENDsript: Analyse and generate multiple output from a PDB 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.
HLAV3D: HLA Squence Variability in 3D A tool that creates a three dimensional representation of variability in HLA molecules

Tools mirroed by Dr. Reche's Immunomedicine Group at the Facultad de Medicina de la Universidad Complutense de Madrid. SPAIN
Rankpep
Sequence Variability and Consensus Plots
Antigenic Peptide Prediction
E-Northern
PEPVAC
NCBI-Blast
PSI-Blast
GenScan
SeqLogo
Dachis
Methylator
SMS
BLAST2FASTA
SVA
EMBOSS
H2PDB
MSAT
ESPript 2.0
ENDscript 1.0
HLAV3D

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