Genome Sequencing Isn't Perfect
In “Genome Assembly as Shortest Superstring”, we introduce the problem of assembling a genome from a collection of reads. Even though genome sequencing is a multi-billion dollar enterprise, sequencing machines that identify reads still produce errors a substantial percentage of the time. To make matters worse, these errors are unpredictable; it is difficult to determine if the machine has made an error, let alone where in the read the error has occurred. For this reason, error correction in reads is typically a vital first step in genome assembly.
As is the case with point mutations, the most common type of sequencing error occurs when a single nucleotide from a read is interpreted incorrectly.
Given: A collection of up to 1000 reads of equal length (at most 50 bp) in FASTA format.
Some of these reads were generated with a single-nucleotide error.
For each read
Return: A list of all corrections in the form "[old read]->[new read]". (Each correction must be a single symbol substitution, and you may return the corrections in any order.)
>Rosalind_52 TCATC >Rosalind_44 TTCAT >Rosalind_68 TCATC >Rosalind_28 TGAAA >Rosalind_95 GAGGA >Rosalind_66 TTTCA >Rosalind_33 ATCAA >Rosalind_21 TTGAT >Rosalind_18 TTTCC
TTCAT->TTGAT GAGGA->GATGA TTTCC->TTTCA