Cluster short, homogeneous strings (DNA) according to common substructures and extract consensus classes

Question

Objective:
group a large pool of short DNA fragments into classes that share common subsequence patterns and find the consensus sequence of each class.

• Pool: approx. 300 sequence fragments
• 8 - 20 letters per fragment
• 4 possible letters: a, g, t, c
• each fragment is structured in three regions:
  • 5 common letters
  • 8 or more g and c positions
  • 5 common letters
    (Like a regular expression that would be [gcta]{5}[gc]{8,}[gcta]{5})

Plan:
to perform multiple alignment (i.e. with ClustalW2) to search for classes that have common sequences in area 2 and their consensus sequences.

Questions:

• ?
• 2 , , ?
• ?

,

Answer 1

, 300 FAR TOO FEW , , 8-. 65 536 8- 3 000 000 000 ( , , ). G/C, 3 000 000 000/65 536 * 2 ^ 8 = ~ 12 000 000 (, , , CpG ). 300?

. 1, CG GC , -G--C. , ( ). .

Clustal - , . GC, :

• G/C 8-mer ( 2 ^ 8 = 256).
• GC- , , 8- .
• GC- .

8-mer , . .

Answer 2

, , , (, ).