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Tools

 
NCBI (National Center for Biotechnology Information) Includes various databases that give access to protein and genomic information
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BLAST (Basic Local Alignment Search Tool) a bioinformatics tool used to compare amino acid, DNA, or RNA sequences
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NCBI AceView is a comprehensive database that contains all public mRNA sequences, mainly from GenBank and RefSeq, as well as cDNA sequences from dbEST and Trace
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UniProt is a large database of protein sequence information
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Bgee is a database for comparing multiple types of genetic data across multiple species
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Pfam is a database of protein families
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PLOS ONE is a database of peer reviewed scientific journals
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RCSB PDB  (Protein Data Bank) incorporates information about 3D structures of proteins as well as nucleic acids
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OMIM (Online Mendelian Inheritance in Man) is a database that has a large store of information concerning genetic disorders in humans
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PDBJ (Protein Data Bank of Japan) is a Japanese based database of proteins
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GeneCards is a database of human genes
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Ensembl is a genome browser that is comprised of information relating to genomics and predictions in regulatory function
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KEGG is a bioinformatics database dealing mainly with biological pathways, based in Japan

Methods

A purified protein from molecular sieve gel filtration, ion exchange, and affinity chromatography was used to create a partial amino acid sequence. We ran this sequence through the NCBI’s BLAST program to determine that the protein in question is XPA. From the protein NCBI page we were able to also find the gene and mRNA information. Using the AceView database, we found information on the isoforms of XPA. This site also was used to find the information on TSS, TATA box, CCATT box, GC box, initiators, introns, exons, and Poly-A signal sites.
 
The structure of the protein was found using the RCSB PDB and visualized using NCBI’s iCn3D web program. RCSB PDB and PDBsum were used to find functional domains, subdomains, and structural motifs. We utilized UniProt, KEGG, PLOS ONE, and NCBI PubMed Central (PMC) in order to determine protein functions of XPA. These databases shed light on the minutiae of the protein function, down to the molecular level.
 
Much of our research focused on the most important functions of XPA, base excision repair and damaged DNA binding. We also found major biochemical pathways of  XPA’s role in platinum drug resistance and nucleotide excision repair. HPRD and Bgee were used to find what tissues XPA is expressed in and at what stages of development. Mutation information was found using OMIM and PubMed. XPA is involved in DNA repair, so most of the diseases were various types of cancer. The only other type of disease researched was xeroderma pigmentosum, an autosomal recessive disorder that causes a decrease in efficacy of XPA.
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