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Sanger Sequencing

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DNA sequencing is a fundamental technique that is routinely used in the biological sciences. This method can be applied to a range of questions at different scales - from the sequencing of a cloned DNA fragment or the study of a mutation in a gene up to whole-genome sequencing. However, despite the widespread use of sequencing today, it was not until 1977 that Fredrick Sanger and his collaborators developed the chain-termination method to decode DNA sequences. It relies on the separation of a...

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A contig assembly program based on sensitive detection of fragment overlaps.

¹Department of Computer Science, Michigan Technological University, Houghton 49931.

|September 1, 1992

Summary

A new computer program, the contig assembly program (CAP), efficiently assembles DNA fragments using filtering, dynamic programming, and a greedy approach. It successfully processed genomic sequencing data, demonstrating its effectiveness in DNA fragment assembly.

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Novel Sequence Discovery by Subtractive Genomics

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Published on: January 25, 2019

Area of Science:

Bioinformatics
Computational Biology
Genomics

Background:

Assembling short DNA fragments into longer contiguous sequences (contigs) is a critical step in genomic sequencing.
Existing assembly methods face challenges with sequencing errors and repetitive DNA sequences.

Purpose of the Study:

To develop an effective and efficient computer program for DNA fragment assembly.
To improve the accuracy and speed of contig generation in genomic projects.

Main Methods:

Developed the contig assembly program (CAP), incorporating a filtering step to remove non-overlapping fragment pairs.
Utilized a dynamic programming algorithm for maximal-scoring overlapping alignment, optimized for sequencing errors and repetitive sequences.
Employed a greedy approach to assemble fragments based on alignment scores.

Main Results:

The CAP program demonstrated satisfactory performance on fragment data from genomic sequencing projects.
Achieved efficient computation time and memory usage, assembling 1015 fragments into long contigs in approximately 4 hours on a Sun workstation.

Conclusions:

The contig assembly program (CAP) provides an effective and efficient solution for DNA fragment assembly.
CAP's methodology is robust in handling sequencing errors and repetitive elements, crucial for large-scale genomic analyses.