Sequence File Format And Sequence Assembly - Lecture Slide - Biology 2, Slides of Biology

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Automated creation of contigs

 Steps

1. Finding pairwise overlaps

2. Resolving overlaps

3. Improving alignment

4. Final assembly and consensus generation

1. Finding pairwise overlaps

 Compare each fragment (and its

complement) with each other fragment

 Generate list of regions of similarity that

meet criteria below

Parameters

 minimum overlap length (default 20)  stringency (% of bases that must match, default 70)  minimum repeat length (default 30)

2. Resolving overlaps

 Build larger pieces by combining overlaps

2. Resolving overlaps

 Build larger pieces by combining overlaps

2. Resolving overlaps

 Build larger pieces by combining overlaps

2. Resolving overlaps

 Build larger pieces by combining overlaps

2. Resolving overlaps

 Build larger pieces by combining overlaps

3. Improve alignment

 Introduce gaps in sequences if they will

improve overlaps

alignment parameters

 gap creation penalty (default 2.0)  gap extension penalty (default (0.1)

Manual consensus editing

 Crucial to verify alignment and resolve

ambiguities (e.g., sequencing errors)

 Program keeps an “edit history” that tracks

all changes made to the original sequences:

essential to be able to “retrace your steps”

from original sequencing gels (e.g., in case

of conflicts with sequences in database)

AssemblyLIGN Tutorial

 Open “demo π” project