1. LMO1
940511

2. A. Information
1. Sequence:
Human – base pair. Ensembl ID = ENSG
Mouse – base pair. Ensembl ID = ENSMUSG
Rat – 4748 base pair. Ensembl ID = ENSRNOG
2. Downloaded from: Ensembl.org
3. Regions: LMO1.
4. Reference:
Ivan et al. ECR Browser. Nucleic Acids Research. 32,
Ivan et al. Mulan. Genome Research. 15: 1-11.
Mathieu et al. Alignment Multiple Genomic Sequences With the Threaded
Blockset Aligner. Genome Research. 14:
5. Alignment information ( including tools, scoring systems, guiding trees, and so on ) :
Tools: Multiple alignment – ClustalW, MAVID, MLAGAN
Pairwise alignment – AVID, LAGAN
Local alignment – TBA/MULTIZ
6. Note: base pairs are added at both 5’ and 3’ end.

3. B. Comparison by percent identity plot
Clustal, MAVID, and MLAGAN between Human, Mouse, and Rat
Position:

4. A stacked-bar chart
The pie charts
ClustalW
MAVID
MLAGAN

5. Phylogenetic tree
for ClustalW
Phylogenetic tree
for both MAVID
and MLAGAN

6. B. Comparison by percent identity plot
Clustal, MAVID, and MLAGAN between Human and Mouse
Position:

7. A stacked-bar chart
The pie charts
ClustalW
MAVID
MLAGAN

8. Phylogenetic tree for ClustalW
Phylogenetic tree for both MAVID and MLAGAN

9. B. Comparison by percent identity plot
Clustal, MAVID, and MLAGAN between Human and Rat
Position:

10. A stacked-bar chart
The pie charts
ClustalW
MAVID
MLAGAN

11. Phylogenetic tree for ClustalW
Phylogenetic tree for both MAVID and MLAGAN

12. B. Comparison by percent identity plot
Clustal, MAVID, and MLAGAN between Mouse and Rat
Position:

13. A stacked-bar chart
The pie charts
ClustalW
MAVID
MLAGAN

14. Phylogenetic tree for ClustalW
Phylogenetic tree for both MAVID and MLAGAN

15. AVID and Lagan between Human and Mouse
Position:

16. A stacked-bar chart
The pie charts
AVID
LAGAN

17. AVID and Lagan between Human and Rat
Position:

18. A stacked-bar chart
The pie charts
AVID
LAGAN

19. AVID and Lagan between Mouse and Rat
Position:

20. A stacked-bar chart
The pie charts
AVID
LAGAN

21. TBA/MULTIZ between Human and Mouse
Position:
A stacked-bar chart
The pie charts

22. TBA/MULTIZ between Human and Rat
Position:
A stacked-bar chart
The pie charts

23. TBA/MULTIZ between Mouse and Rat
Position:
A stacked-bar chart
The pie charts

24. Some Comparison between results that are generated by different algorithm
Clustal, MAVID, and MLAGAN between Human, Mouse, and Rat
Clustal, MAVID, and MLAGAN between Human and Mouse

25. Clustal, MAVID, and MLAGAN between Human, Mouse, and Rat
Clustal, MAVID, and MLAGAN between Human and Rat

26. Clustal, MAVID, and MLAGAN between Human, Mouse, and Rat
Clustal, MAVID, and MLAGAN between Mouse and Rat

27. Clustal, MAVID, and MLAGAN between Human and Mouse
AVID and Lagan between Human and Mouse
TBA/MULTIZ between Human and Mouse

28. Clustal, MAVID, and MLAGAN between Human and Rat
AVID and Lagan between Human and Rat
TBA/MULTIZ between Human and Rat

29. Clustal, MAVID, and MLAGAN between Mouse and Rat
AVID and Lagan between Mouse and Rat
TBA/MULTIZ between Mouse and Rat