Assembling DNA Fragments with a Distributed Genetic Algorithm - Parallel Computing for Bioinformatics and Computational Biology - page 288

Figure 12.1 Graphical representation of DNA sequencing and assembly [10].
2. Base Call Errors . There are three types of base call errors: substitution,
insertion, and deletion. They occur due to experimental errors in the elec-
trophoresis procedure. Errors affect the detection of fragment overlaps. Hence,
the consensus determination requires multiple alignments in high coverage
regions.
3. Incomplete Coverage . It happens when the algorithm is not able to assemble a
given set of fragments into a single contig.
4. Repeated Regions . Repeats are sequences that appear two or more times in
the target DNA. Repeated regions have caused problems in many genome-
sequencing projects, and none of the current assembly programs can handle
them perfectly.
5. Chimeras and Contamination . Chimeras arise when two fragments that are not
adjacent or overlapping on the target molecule join together into one fragment.
Contamination occurs due to the incomplete purification of the fragment from
the vector DNA.
After the order was determined, the progressive alignment algorithm is applied to
combine all the pairwise alignments obtained in the overlap phase.