Algorithms


Computers are responsible for the DNA searching, alignment, and sequence reassembly; their involvement has greatly improved genome identification results in terms of speed, efficiency, and accuracy.


Database searching

In the realm of database searching, computers take scanned data and use one of the specified algorithms to search the target database for the query sequence. This is not as simple as it sounds, and was vital to the sequencing of the genome. BLAST, FastA, and Smith-Waterman are all examples of such algorithms.


Sequencing Standards

Phred and phrap are often used in tandem for large scale sequencing. Phred interprets a DNA trace for its bases and the probable error. Phrap attempts to sequence fragments.


Others

Dynamic programming is a key technique in alignment.
Greedy Sequence Reassembly algorithms are similar to the Traveling Salesman Problem.
Local Scoring Matrices are essential to algorithms such as BLAST.



Dynamic Programming   Scoring Matrices
Smith-Waterman BLAST FastA
Phred   Phrap
  Sequence Reassembly