2 Humans vs. Neanderthals In the last lab, we learned how to obtain protein sequences from UniProt. Another important sequence database is the NCBI database. Like UniProt, NCBI is made up of sub-databases. Figure 2 shows the diferent databases that are a part of NCBI. In this lab, well use the Nucleotide database to get DNA sequences from NCBI. If youd like to know more about what you can do with with NCBI, see these tutorials. We compare the nucleotide sequences for a mitochondrial gene (COX2) in human and neanderthal [1]. To begin with, we need to get FASTA sequence for Homo sapiens and neanderthal COX2. Go to https://www.ncbi.nlm.nih.gov/ and choose Taxonomy from the drop down menu next to the search bar. Click Search. Go to Extinct Organisms. Find Homo sapiens neanderthalensis (neanderthal man). On the right side of the page on neanderthal man, you can fnd Entrez Records. We are looking for the COX2 gene, so click on Gene. On the page youre redirected to, fnd the COX2 gene. You can get the FASTA sequence for this gene by looking under the Genomic regions, transcripts and products section of the page for COX2. 1. What is the Gene ID for COX2 for neanderthal man? 2. Find the Gene ID for the COX2 gene in modern man (Homo sapiens). (Make sure it is the mitochon drially encoded one.) 3. Get the FASTA sequences for human and neanderthal COX2 genes. Run a pairwise sequence alignment using these nucleotide sequences and this online tool called Emboss-needle. Report the percent identity these sequences show. 4. Comment on the results. Do you observe anything interesting?

OMIM Genome GEO PopSet PubMed Rudolce Protein SNP (Domans UNSTS Structure 1000's 10,000's 100.000 1,000,000 10,000,000 Figure 2: Relationships between databases in NCBI