CISC 4020 Bioinformatics
Monday, April 19, 2010
Lab Exercise #7: Genomics / Human Genome and Diseases
(due April 26 – submit on Blackboard)
(1) Genomic BLAST
Human mitochondrial DNA (RefSeq identifier NC_012920) has a bacterial origin.
1. Use Genomic BLAST to compare Human mitochondrial DNA against all bacteria
genomes. (On the NCBI BLAST page, under BLAST Assembled Genomes, choose
Microbes). To which group of bacteria is the human sequence most related?
2. To which genes is the human sequence most related?
3. There is just one bacterial protein that is related to the proteins encoded by the human
mitochondrial genome. What is it? (To search specifically for proteins encoded by
human mitochondrial DNA, use NC_012920 as a query in either genomic BLAST (change
the database you are searching from DNA to protein) or in a blastx search restricted to
bacteria).
(2) HomoloGene / UCSC Genome Browser
Some human disease alleles correspond to the wild-type sequence of closely related
chimpanzee and/or rhesus macaque proteins. Align the human, macaque (Rhesus
macaque), chimpanzee (Pan troglodytes), rat (Rattus norvegicus), and mouse (Mus
musculus) sequences for the proteins encoded by the following genes. For each, the
description N > A:CHMT refers to the consensus human amino acid N (normal), the disease
associated form A (altered), C (chimpanzee), H (inferred human/chimpanzee ancestor), M
(rhesus macaque), T (inferred human/rhesus ancestor using mouse and dog as outgroup
species).
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ABCA4 (Stargardt disease; chromosome 1), R > Q:RRQR; H > R:RRRR
CFTR (cystic fibrosis; chromosome 7), F > L:FFLL; K > R:KKRK
PAH (phenylketonuria; chromosome 12), Y > H:YYHY; I > T:IITI
OTC (ornithine hyperammonemia; chromosome X), R > H:RRHH; T > M:MTTT
Alignments can be found in the HomoloGene project at NCBI and the comparative genomics
tracks at the UCSC Genome Browser.
(3) More on OMIM
Choose any disease you will like to investigate and use OMIM to gather any information that
you think is useful such as: phenotype, related genes / mutations, chromosome / location, etc.
(Refer to prior lab question on OMIM).