Here we showcase student projects from courses related to our Bioinformatics, MS program. More projects will be added in the coming weeks.
Guided Studies in Bioinformatics, BI7583
Pipeline for SNP Detection | Ernest Szeto, Summer 2010
About the Project
The advent of inexpensive short reads sequencing technology has made the detection of SNPs (Single Nucleotide Polymorphism) more widely available.
In this project, we take Solexa reads, align them with a well curated finished Yeast genome for the purpose of detecting mutated genes. The amino acid mutation as a result of the SNP is indicated.
A pipeline has been developed for mapping reads to reference genes in a reference genome for purposes of SNP detection. A pipeline provides a systematic framework for analyzing multiple data sets dealing with the same problem.
Because bioinformatic data can be noisy, quantitative techniques are used for ranking the candidates for gene mutation. In this case, the percentage coverage and depth (percCov, depth) for producing the ranked candidate list. The candidate list is made available for human inspection to ascertain the the biological meaning of the SNP candidates. The list is annotated with gene product name, amino acid change, and Pfam domain affected to aid in the interpretation.