Genome / DNA Base-Calling Project

http://stat.fsu.edu/~lilei/lilei/research/basecall.html

Sanger's sequencing 기술은 효소 반응, 전기 이동, 형광에 기초한 발견 기술의 조합이다.

이 Diagram은 Sanger's sequencing의 구조의 기본 아이디어를 설명해준다. 이 절차는 형광물질의 강도에 따라 시간 흐름에 따라 4개의 컴포넌트(A,C,G,T)로 구성해 나간다.

Base-calling은 large-scale genomic sequencing 노력의 큰 부분이다.

The following flow chart depicts the struture of our model and base-calling strategy.

We are really trying to mimic the DNA sequencing procedure by this statistical model. Namely, given a DNA sequence, we can generate from this model a virtual sequencing trace signal, which shows quite a lot of similarity to the real data. Here is one example. More examples of simulated base-calling can be found in Simon's homepage.

My current research on DNA base-calling mainly concerns three topics: hidden Markov models, deconvolution, color separation. Five manuscripts have arisen from this research. My dissertation will be a collection of these manuscripts. More details are given by the following titles and summaries.

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Phred base-calling is a computer program for identifying a base (nucleobase) sequence from a fluorescence "trace" data generated by an automated DNA sequencer that uses electrophoresis and 4-fluorescent dye method.