Skip to content
Sequence Alignment Algorithm (Dynamic Programming)
Scilab
Branch: master
Clone or download
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Permalink
Type Name Latest commit message Commit time
Failed to load latest commit information.
Images
fasta
protein
NJ Tree.newick
README.md
WPGMA Tree.newick
bm4321_assignment_1_150005r_1.sce
bm4321_gene_prom_region.sce
bm4321_sequence_alignment_func.sce
bm4321_statistical_alignment_new.sce

README.md

Bioinformatics-Genomic-signal-processing-

NZ_CP014692.1 Acetobacter aceti

Overview of the protein gene chosen to be common in all the accessions of bacterial species

Adenosylhomocysteinase

Is an enzyme that converts S-adenosylhomocysteine to homocysteine and adenosine. This enzyme catalyses the following chemical reaction
S-adenosyl-L-homocysteine + H2O ⇌ L-homocysteine + adenosine
The enzyme contains one tightly bound NAD+ per subunit.

Distance Matrix

Phylogenetic Trees

WMPGA Tree

Given below is the Newick Format of the WPGMA output tree. In this format, the number following the organism or group denotes the distance to its parent
((((((NZ_CP022699.1/CP022699.1:0.50,NZ_LN606600.1/LN606600.1:0.50):5,NZ_CP014687.1/CP0146 87.1:5.50):0.57,((((NZ_CP015164.1:0.00,NZ_CP015168.1:0.00):0,NZ_CP021524.1:0.00):1,((((((((NC_0 17150.1/AP011163.1:0.00,NC_017108.1/AP011170.1:0.00):0,NC_013209.1/AP011121.1:0.00):0,NC_017 125.1/AP011142.1:0.00):0,NC_017100.1/AP011128.1:0.00):0,NC_017121.1/AP011135.1:0.00):0,NC_01 7146.1/AP011149.1:0.00):0,NC_017111.1/AP011156.1:0.00):0,NZ_AP014881.1/AP014881.1:0.00):1):0. 47,((NZ_CP022374.1/CP022374.1:0.00,NZ_CP023189.1/CP023189.1:0.00):0.25,(NZ_CP023657.1/CP02 3657.1:0.00,NZ_CP011120.1/CP011120.1:0.00):0.25):1.22):4.6):0.37,NZ_LN609302.1:6.44):0.53,NZ_A P018515.1/AP018515.1:6.97):3.12,NZ_CP014692.1:10.09)

Discussion

When we considering the WPGMA, it assumes constant rate of evolution. Therefore, the distance from the root to leaf nodes are equal in length. This can be observed by the above figure.

  • When we observe the accession numbers corresponding to Acetobacter oryzifermentans and Acetobacter pomorum we can observe that they are branched from the common node. So that they are evolved from a common ancestor. So that there is a complete or almost complete similar in between different strains of their own species.

  • When we observe the accession numbers corresponding to acetobacter tropicalis and acetobacter senaglensis, there is a significant similarity. Therefore we can assume that they have performed some amount of acquiring of genes through horizontal gene transfer

  • We can observe that Acetobacter aceti seems to involve independently, from the most initial ancestor of this phylogenetic tree, and it has the maximum genetic tree. The reason for that is it has not undergone any stage of gene transfer with the other species in its genus.

Neighbour Joining Tree

Given below is the Newick Format of the NJ output tree. In this format, the number following the organism or group denotes the distance to its parent.

((((((((((((((NZ_CP022374.1/CP022374.1:0.00,NZ_CP023189.1/CP023189.1:0.00):0.08,NZ_CP011120.1 /CP011120.1:- 0.08):0.23,NZ_CP023657.1/CP023657.1:0.27):1.49,(((NZ_AP018515.1/AP018515.1:7.81,NZ_LN609302 .1:5.19):0.59,(NZ_CP014687.1/CP014687.1:4.21,NZ_CP014692.1:12.79):1.41):0.41,(NZ_CP022699.1/CP02 2699.1:0.75,NZ_LN606600.1/LN606600.1:0.25):4.84):4.92):0.33,((NZ_CP015168.1:0.00,NZ_CP021524.1:0. 00):0.02,NZ_CP015164.1:-0.02):1.12):0.84,NZ_AP014881.1/AP014881.1:- 0.05):0.05,NC_017150.1/AP011163.1:0.00):0.00,NC_017108.1/AP011170.1:0.00):0.00,NC_013209.1/AP 011121.1:0.00):0.00,NC_017125.1/AP011142.1:0.00):0.00,NC_017100.1/AP011128.1:0.00):0.00,NC_017 121.1/AP011135.1:0.00):0.00,NC_017146.1/AP011149.1:0.00),NC_017111.1/AP011156.1:0)

Discussion

The tips of the branches in the Neighbor-joining tree does not align with each other, the reason for that is constant rate of evolution is not assumed here, as opposed to the WPGMA tree. Neighbour-joining algorithm commonly used for the construct phylogenetic trees. When create phylogenetic tree we considered the distance from one organism to all the other organisms. Further create tree using identity matrix due values are normalized.

  • In the NJ tree, Acetobacter pasteurianus have branched immediately after the earliest common ancestor. Further we can see that genetic distance is very small compared to others.
  • When we observe accession numbers of Acetobacter oryzifermentans and Acetobacter pomorum pattern similar to that of WPGMA tree observed. So that we can conclude a possibility of horizontal transfer gene.
  • Acetobacter ghanensis, Acetobacter persici, Acetobacter aceti, Acetobacter orientalis all have evolved from the same ancestor, but have long genetic distance.
  • Acetobacter tropicalis, Acetobacter seneglensis appears to be having significant amount of similarity as distance are very closer.

Conclusion

The WPGMA and the NJ trees are used to study gene evolution. When we compare WPGMA tree and NJ tree, NJ tree provides better results that the WPGMA tree. With the above observations we can come in to following conclusions.

  • Acetobacter oryzifermentans and Acetobacter pomorum have undergone horizontal gene transfer
  • Acetobacter ghanensis, Acetobacter persici, Acetobacter aceti, Acetobacter orientalis have undergone horizontal gene transfer.

References

  1. https://en.wikipedia.org/wiki/Adenosylhomocysteinase
  2. Newick Standard for representing trees. [Online]. Available: http://evolution.genetics.washington.edu/phylip/newicktree.html
  3. Figtree Software, 2018. [Online]. Available: http://tree.bio.ed.ac.uk/software/figtree/
You can’t perform that action at this time.