Labwork 1

DATABASE
Practice 1

• Deadline:
• before 17:00 via Blackboard
• submit the .pdf file with name “Lab1_Bioinfor_student’sID.pdf”
1/ ORF(s) of a gene sequence

- Search for tool(s) which is(are) used to find ORF of a sequence

- List name of tools that you found, as many as you can, including picture
of homepage. Website address
- Which one will you use? Why?
- Show all of the ORFs of the sequence Lab1_ORF.txt by your chosen
tool. Explain the parameters you chose
- Choose another tool to find ORFs of the sequence. Compare the result
with previous one
 2/ GenBank (NCBI)

- Go to GenBank website: https://www.ncbi.nlm.nih.gov/genbank/

- Find the scientific name of “one thing” which your are interested in, for
example: pineapple, orange, human, rabbit…
- Search for whole genome of that “thing”
 Show all present Chomosome(s) with size, protein, gene,
pseudogene
- Choose one ID at RefSeg column, get detail information of that ID
 ID, Name, Source, List of references, Any comment(s)
 Do they have Hairpin structure, CRE element, Exon? Where
is(are) its(their) position(s)?
 Present the gene map
3/ RCSB PDB
- Go to RCSB PDB website: https://www.rcsb.org/
- Choose 1 protein from the previous question
- Search for 2 3D structures created by X-ray diffraction method of those
proteins
 Report ID, Name and picture of Structure
 Collect sequences in Fasta format
 Compare the quality between 2 structures using Resolution
value and wwwPDB Validation table