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Main.ImperfectRepeats History
Hide minor edits - Show changes to output
November 08, 2006, at 10:13 PM
by Angie -
Changed lines 5-7 from:
most programs compute imperfect repeat under 1)the Hamming distance model (only substitutions), others apply 2) the Edit distance model (substitutions, instertions, deletions)
to:
most programs compute imperfect repeat under 1) the Hamming distance model (only substitutions), others apply 2) the Edit distance model (substitutions, instertions, deletions)
November 08, 2006, at 10:12 PM
by Angie -
Changed lines 3-4 from:
= microsatellites containing mutations (substitution, insertion, deletions)\\ to:
= microsatellites containing mutations (substitution, insertion, deletions)
Changed lines 14-17 from:
- as minimum or average alignment score of two neighbouring copies over the entire array\\
- as minimum or average alignment score of two random copies within the array
to:
- as average alignment score of two neighbouring copies over the entire array\\
- as average alignment score of two random copies within the array
November 08, 2006, at 10:10 PM
by Angie -
Changed lines 8-10 from:
'''
similarity (or number of mutations) can be measured in several ways:'''
to:
'''similarity (or number of mutations) can be measured in several ways:'''
November 08, 2006, at 10:09 PM
by Angie -
Changed lines 8-10 from:
similarity (or number of mutations) can be measured in several ways:
to:
'''
similarity (or number of mutations) can be measured in several ways:'''
Changed line 17 from:
to:
November 08, 2006, at 10:07 PM
by Angie -
Added lines 1-21:
!! Imperfect repeats
= microsatellites containing mutations (substitution, insertion, deletions)\\
most programs compute imperfect repeat under 1)the Hamming distance model (only substitutions), others apply 2) the Edit distance model (substitutions, instertions, deletions)
-> e.g. 1) ACACACA%red%T%%ACA or, 2) ATGCATGC%blue%T%%ATGCATG%red%C%%ATGC
similarity (or number of mutations) can be measured in several ways:
- every n-th nucleotide is a mismatch\\
- as average alignment score of all copies to a computed consensus sequence\\
- as minimum or average alignment score of two neighbouring copies over the entire array\\
- as minimum or average alignment score of two random copies within the array
programs
- search strategy: heuristic?!, modelling, autocorrelation\\
- filter: statistical criteria, E-value, p-value, biological significance
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