ACTIVE LEARNING ACTIVITY 1 BMS551 PRINCIPLES OF BIOINFORMATICS

Title: Searching for homologous sequence from the database

Objective:

1. Learn about searching for homologous sequence in the biological database

2. Understand the concept of data entry and its format
3. Able to do other searching activities using an existing database.

Methodology

A. Concept of biological database and their component

Let us say we want to study Homo sapiens pancreatic lipase. Go to the Genbank website at
www.ncbi.nlm.gov/Genbank/. Observe the Genbank flat-file format. Pay special attention to the
Header, Feature Table and the Nucleotide Sequence Section. Answer the following questions:

(a) How long is the nucleotide sequence in bp?

(b) Where is the site of expression and its locus?
(c) Describe the motif found from this sequence?
(d) Describe the DNA (and the ORF) and protein sequences.
(e) What is the molecular weight of this pancreatic lipase?
(f) What is the OMIM ID?
(g) Check the structure of this entry

Exercise

Use the same method to study homo sapiens adiponectin gene (ADIPOQ) C1Q and collagen domain
that involved with metabolic and hormonal processes in human such as diabetes mellitus etc.
Answer the following question regarding these gene

(a) What is the accession no of this gene? Choose RefSeqGene menu

(b) How long is the nucleotide sequence in bp?
(c) Where is the site of expression and its locus?
(d) Describe the conserved motif found from this sequence?
(e) Describe the DNA (and the ORF) and protein sequences.
(f) What is the molecular weight of this adiponectin gene? Investigate in
RefSeqproteins (2)
(g) What is the OMIM ID?
(h) Check the 3D structure of trimeric globular domain of Adiponectin gene
 B. Searching gene info using taxonomy browser (Ensemble) at
http://asia.ensemble.org/index.html

1. Let us try to explore the Homo sapiens genome. Go to http://asia.ensembl.org/index.html

2. Click under favourite human genome. You can view a karyotype on the right side of the
genome browser. Here you can see 22 autosomal chromosomes with two sexual
chromosome X, Y and MT of human chromosome.
3. You can click on any chromosome for a closer view. Let us investigate on chromosome 18
at the first dark band of its q arm (long arm). Mark region on 18:27461280-27561286 and
investigate its gene content by adding the specific location of the gene at the location box
below the region in details row.
4. Click on the specific gene (purple bar) and get a consolidated view of known Genes, %GC,
SNPs of Chromosome 18 long arm (q).
5. Click on the q11.1 region of the chromosome 18. You will get the contig map of
Chromosome 18 between and 27461280 and 27561286 base pairs.
6. By pointing your mouse pointer on the Overview region, you will find the tool tip Click for
menu on certain regions. If you click on the region where the tool tip does not appear, you
will get the current zoom and the options of changing the zoom image.
7. On clicking any of the Ensemble or EST gene, you will get information like gene name, gene
ID, position in bp, length and gene type. If you click on any of the contig band, you will get
various options of contig, clone, and supercontig.
8. Detailed view has several drop-down options, which you can check on your own, other
than the click for menu and zooming options as in Overview region.
9. Click ENSG00000263611 to explore Ensemble Protein Report.

Exercise

1. Go to Ensemble server and browse Saccharomyces cerevisiae genome under ‘Other species’.
Answer the following question about this fungus.

a) Give the information for length in bp, known protein-coding genes, mRNA genes, rRNA
genes and tRNA genes of chromosome mito.
Prepare a gene report of Saccharomyces Gene Database (SGD) ID tP(UGG)Q.

b) What are the gene type?

c) Determine its location.