This web page was produced as an assignment for Genetics 564, an undergraduate course at UW-Madison.
Protein homology
Homology is the similarity of a DNA sequence across several organisms and species [1]. In this case, homology is used to discuss the similarities of presenilin 1 protein (PSEN1) observed. Much like gene homology, protein homology can be used to narrow down the list of potential model organisms, while also providing a deeper understanding of how the protein will function.
Similar to how the gene homologs were found, an initial search on HomoloGene can prove to be quite useful. Homologene contains a large database of homology groups from various gene sequence data sets that can then be used for model organism comparison. Should HomoloGene fail to provide enough information, BLAST can also be utilized to compare the homo sapiens, or human, mRNA sequence to the chosen FASTA sequence [2]. Another option for finding protein homologs is to utilize Uniprot, a database of proteins and sequences for various species. Information on Uniprot includes the protein, its FASTA sequence, accession number, and can be used to identify percent similarity with a BLAST search[3].
Using the list of homologs for PSEN1, the presenilin 1 gene, an organism list of homologs for PSEN1 was constructed. Though smaller, the protein homologs consist of various organisms and species with consistency to human PSEN1 and the chosen model organisms, mice and zebrafish.
Similar to how the gene homologs were found, an initial search on HomoloGene can prove to be quite useful. Homologene contains a large database of homology groups from various gene sequence data sets that can then be used for model organism comparison. Should HomoloGene fail to provide enough information, BLAST can also be utilized to compare the homo sapiens, or human, mRNA sequence to the chosen FASTA sequence [2]. Another option for finding protein homologs is to utilize Uniprot, a database of proteins and sequences for various species. Information on Uniprot includes the protein, its FASTA sequence, accession number, and can be used to identify percent similarity with a BLAST search[3].
Using the list of homologs for PSEN1, the presenilin 1 gene, an organism list of homologs for PSEN1 was constructed. Though smaller, the protein homologs consist of various organisms and species with consistency to human PSEN1 and the chosen model organisms, mice and zebrafish.
psen1 model organisms
discussion
Though the list above is smaller, the importance of protein homology is stressed all the same. Observing how similar proteins are across species proves to be invaluable in choosing model organisms for future experiments, but also useful in constructing protein domains to illustrate these similarities. For information on the presenilin protein domain, click here. Despite being more selective, this list similarly condones the importance of presenilin 1, both the gene and protein, through various organisms and species. While the similarities observed aren't surprising (as they are all mammals), this protein homology is and has been proven useful in future research regarding Alzheimer's and other neurological genetic diseases alike.
REFERENCES