BT203IU Bioinformatics

Assignment 4

Gene prediction

Due date: 21:00, 8 Apr. 2020

(Submission via email: bioinforsem21920@gmail.com)

Question 1: In the NCBI database, retrieve the nucleotide sequences NG011676. Report:

a. Gene name, database name.

b. Number of exons and its position (the start and the end of each exon).
c. The start and the end of coding region (CDS)
d. Accession number of protein from this gene and the length of polypeptide.

Question 2: Use NG011676 to run GenScan. Report the results and compare the results with
information of this gene from Question 1.
Question 3: Use NG011676 to run FGENESH with selecting of Homo sapiens as organism
specific gene-finding parameters. Report the results and compare the results with information of this
gene from Question 1.

Question 4: Run FGENESB to predict potential genes in an unknown sequence (download at

Blackboard/Assignments/Ass 4_Unknown sequence), choose BACTERIAL generic as a closest
organism. Report:
a. The length of sequence
b. Number of predicted genes, number of transcription units & operons

Navigate to the BLAST homepage and select a protein BLAST (BLASTP). Enter the polypeptide
translated from gene_13 that annotated by FGENESB into the query box and hit the BLAST button.
Report:

c. The start and end of CDS of gene_13

d. Results of BLASTP: max score, e-value, identity, accession number, length of polypeptide,
organism name