The DNA Sequence Viewer allows the user to look at the p53 gene at the DNA sequence level. Users can use the viewer to glance through the overall sequence structure, i.e. the intron positions, exon positions and CpG sites of p53. Users can also use the DNA Sequence Viewer to view SNP sites, mutation sites as well as transcription factor binding sites.

The Protein Sequence Viewer is similar to the DNA Sequence viewer, but instead of presenting p53 at the nucleotide level, it presents the p53 gene at the amino acid sequence level. Users can view the amino acid sequence as well as the position of the different domains within the p53 gene. Also included are positions of SNP sites as well as mutation sites.

The Isoform Sequence Viewer allows the user to look at the overall mRNA sequence as well as the coding sequence of the different known isoforms of p53. View the demo clip.

The Mutation Search page allows the user to retrieve known mutation information by querying the p53 knowledgebase. Users can query for mutation based on Nucleotide positions, Codon positions, Mutation types, Mutation effect types, Tumor origins, Morphology, etc. Included in the search results are information like the change in nucleotide or amino-acid if any, affect protein domains as well as the publications that describe the mutation. View the demo clip.

The Polymorphisms page displays all the known SNPs in the p53 knowledgebase. Information about Nucleotide Position, SNP Alleles, SNP Ambiguity, the Polymorphic Nucleotide, the SNP Type, Codon Position and Amino Acid Change are listed. In addition, SNP allele frequencies, their geographical distribution and disease association are displayed. View the demo clip.

The Haplotypes page displays the haplotype blocks of the SNPs in the p53 genomic locus (additional SNPs 50kb upstream and downstream of the locus were also included) predicted by the algorithms provided by the HapBlock program. View the demo clip.

The p53-Related Molecules page allows the user to search for molecules related to p53 in terms of interactions, modification, transcription and more. View the demo clip.

The Transcription Factor page shows the information that is present in the p53 knowledgebase about the transcription factors that bind to the p53 DNA. Details such as the binding molecule, the interaction type, the position on the p53 DNA that the molecule binds as well as the publications that describe the interaction are included. View the demo clip.

The p53 Target Genes page shows the chromosomal locations of p53's target genes binding sites. Details such as the chormosomal location, binding sequence and p53's transcriptional regulation are included. View the demo clip.

The Interactions page list information in the p53 knowledgebase regarding proteins that are known to interact with p53. View the demo clip.

The Monoclonal Antibodies page lists information in the p53 knowledgebase regarding antibodies that are known to target p53. Included in the information are details like the exact region within the p53 protein that the antibodies bind, the immunization antigen used for obtaining the antibodies as well as publications that describe the antibodies. View the demo clip.

The Modifications page lists information in the p53 knowledge base regarding the sites on the p53 protein that are known to undergo post translational modifications. Included in the information are details like the exact amino acid within the p53 protein that undergoes post translational modifications as well as the source in which that information is obtained.

A compendium of pathway maps available on the web can be found here. In addition, links to pathways databases and other resources are given. A pathways database and viewer is being developed by BII scientists in collaboration with BIND (Biomolecular Interaction Database), and will be available soon.

The Structure Viewer allows the user to view existing human p53 PDB structures from the RCSB Protein Data Bank using JMol. PDB structures containing published mutations in the human p53 protein can be linked from their respective mutation entries to this viewer, where the mutated residue is highlighted. View the demo clip.

The user is able to assess the conservation of the p53 genomic DNA sequence across various species through Multiple Sequence Alignment using ClustalW. Users are able to choose the sequences for the Multiple Sequence Alignment and subsequent analysis of the results can be viewed through JalView.

The user is able to assess the conservation of the p53 amino acid sequence across various species through Multiple Sequence Alignment using ClustalW. Users are able to choose the sequences for the Multiple Sequence Alignment and subsequent analysis of the results can be viewed through JalView.

The Structural Mutation Analysis Tool allows the user to perform point mutations on a human p53 wildtype structure and view the results comparatively using JMol. Mutant PDB structures were generated using Swiss PDB Viewer 3.7 by choosing the best rotamer conformation of the mutant amino acid.

The user is able to run a prediction tool to determine the secondary structure of the p53 amino acid sequence across various species. Users are also able to choose the sequences for the prediction.

This tool allows the user to input a sequence to search against the wildtype p53 amino acid / DNA sequence; the results allows the user to return to any of the sequence viewers (DNA and Protein sequence viewers) where the input sequence is at the beginning of the sequence view. View the demo clip.