Project

This page shows the rate progress about my final paper presentation and project for

CS 234 - "Computational Methods for the Analysis of Biomolecular Data."

• February 17

- Choosing my presentation topic "A graph-based approach to systematically reconstruct human transcriptional regulatory modules."

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• February 23

- Choosing my project topic "Benchmarking gene recognition softwares."

- Reading the content of the presentation project; finding some information about the co-expression, microarray databse on the internet

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• February 29

- Found some information about "transcription module", "transcription factors"

- Finding some information about gene prediction

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• March 2

- I found some problem when trying to figure out the formula in the presentation paper (probability, density formula)

- Read papers about Gene Prediction Technology

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• March 4

- Found some "Gene Prediction" Software: GeneScan; GrailXP; GeneMark; Augustu; AMIGene

- I found some problems when coding the Grail, Jigsaw ... some programs which should be implement under Linux System

- Realized what the formula in the paper are

- Got familiar with the software

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• March 7

- I found some problems when making the gene prediction of one certain species' DNA sequence

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• March 14

- Looking for some more definition about gene prediction (annotation technology, HMM, interpolated MM, probability calculating)

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• March 15

- Found more genome datasets (find some DNA with the similar species)

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• March 16

- Found that the gene prediction software should be used in one certain condition

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• March 18

- Looking for some papers about the prediction method

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• March 19

- Try to make the combination and comparison between some prediction result in similar species