Tools

Alignment Analysis tools:

      MUSCLE is a sequence alignment tool who's full name is multiple sequence comparison by log - expectation. MUSCLE improves the algorithm of cluster. Compared with cluster, it has faster running speed and more accurate results.

      SIAS (sequence identity and similarity) is an online analysis tool for calculating protein sequence identity and sequence similarity through a variety of methods.Sias supports files in Clustal, FASTA or GCG / pileup formats. Visitors can choose one of BLOSUM62, PAM250 and GONNET as the calculation method of similarity matrix. Visitors can also manually set the interested select gap penalties.

Computational Immunology tools:

      HLA 3D is a platform for online analysis of sequence variability of HLA molecules. The website shows the sequence alignments of the antigen presenting platform of HLA I and II molecules (A1A2 and A1B1 domains, perspective) from which the variability analyses were performed. And it can also visualize the mapping of HLA sequence variability and its related 3D structure.

      PVS(Protein Variability Server) is an online analysis tool that uses several variability metrics to calculate sequence variability within multiple sequence alignments.And it can perform several tasks, such as masking the variability in the reference sequence, returning conserved fragments or mapping the sequence variability onto a provided 3D-structure. The files it needs include protein sequences and PDB files. Visitors can choose one of Shannon, Simpson and Wu Kabat to calculate sequence variability.

3D-Structure Analysis tools:

      H2PDB is an online protein sequence analysis tool, which can map the amino acid variability within a protein sequence alignment onto a 3D structure . The variability is calculated using the Shannon Entropy equation (H), and it is mapped onto the 3D structure via a B factor. The server requires two inputs: a multiple sequence alignment and a PDB file with the 3D-coordinates of one of the sequences in the alignment. Sequence alignment must be in ClustalW format, and must be edited so that it is ungapped with regard to the sequence for which the 3D coordinates are provided. RES numbering in PDB must be consecutive and without missing or repeated RES numbers.Alignment and PDB files must be in TEXT format.

      MSAT(MODELING AND SOLVENT ACCESSIBILITY TOOL) is an online protein sequence analysis tool, which can identify the hydrophobic residues exposed by solvents in protein sequences and compare them with the residues of closely related sequences, so as to provide useful help for selecting the best residues for site-specific mutagenesis. The steps of using the tool are:
1 Models the 3D-structure the of input sequence (query). Models are produced by SCWRL, using a template obtained from a PSI-BLAST search against the PDB database. Model is only built only if the e-value of the sequence template is < 1e-5. If the template identity to the query is > 95% following calculations are carried out over the template. Insertions and deletions are not modeled in this version of the program.
2. Calculates the Fractional Solvent accessibility of the models using NACCESS
3. Outputs a 3D-model of the query, and a multiple sequence alignment of the query and various close orthologues.