EXERCISE 3

DEADLINE:
BEFORE 17:00 VIA BLACKBOARD
SUBMIT THE .PDF FILE WITH NAME
“LAB3_BIOINFOR_STUDENT’SID.PDF”
1/ GENERAL INFORMATION
- How to find homologous for a gene/protein in
another organism?
- What are the five different BLAST programs? Briefly
describe them in your own words, indicating the
type of query sequence and the type of database
searched?
- With distance matrix, can we know it should be
rooted or unrooted phylogenetic tree?
- When should we use Neighbor Joining algorithm or
Maximum Likelihood method or Maximum
Parsimony?
- What does bootstrap value indicate?
2/ BLAST
Get the nucleotide sequence from the Lab3_BLAST.txt. Do a
MegaBLAST search against the human genome (all
assemblies) database (Use the "genome" database). Ignore
the hits to “alternate assemblies”. Parameters are set as
default.
- What is name of nucleotide sequence?
- Which chromosome(s) gave BLAST hits in your search? Provide
the Expect value, number of mismatches, number of gaps, and
length of alignment. Provide an explanation for the relationship
between the chromosome sequence(s) and given gene.
- Discuss the differences between the BLAST hit on
chromosome(s), if there are more than 1 chromosome.
2/ BLAST (CONT.)
Do the same BLAST search as above of the same sequence,
but use the BLASTN search strategy instead of MegaBLAST.
- Which chromosomes gave BLAST hits in your search?
- Describe the differences in the results from the BLASTN and
MegaBLAST searches. Which search would you use to identify
distantly related sequences?
3/ DRAW PHYLOGENETIC TREE (HANDED)
- By Neighbor Joining algorithm, draw the un-rooted
phylogenetic tree base on this distance matrix.
- Find the outgroup.
4/ CONSTRUCT PHYLOGENETIC TREE
- Use Influenza virus database of NCBI to search for
Human Hemagglutinin (HA) of Influenza A in Vietnam
since 2010
- Collect any 5 HA protein sequences of H1N1
- Perform Multiple alignment using ClustalX / Mega7 /
MegaX (specify your chosen parameters)
- Using same program, construct phylogenetic tree
using Neighbor Joining algorithm and Maximum
Likelihood method (show branch length/bootstrap
value…)
5/ READ PHYLOGENETIC TREE
• How many OTUs in this
Tree?
• Show pairs which have
longest distance and
shortest distance
• Which OTU has large
evolutionary change
compared to common
ancestor ?
• Which OTU has least
evolutionary change
compared to common
ancestor?