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Brian Chan

Former member

Brian Chan

Phone: (530752-2321
Web page:

 Lab member: 2001-2004.
Position Bioinformatics Programmer
Education Double major in Computer Science and Mathematics in UCDavis, expecting to graduate in June 2004
Research Summary

I was hired as an undergrad programmer in my sophomore yearsince April 2001. My main job title is to writestandalone and web interface to process and visualize bioinformatics data.I have learned and become proficient in designing and developing software.I also acquired some amount of bioinformatics knowledge to facilitate thebackground coding of each of my program. Under the supervision ofAlex Kozik,I managed to complete and achieve the following:

DiagHunter and GenoPix2D publication

I played a small part in this project by writing code for theGenoPix2D visualization plot. This paper was published on Genome Biologyon Sept 19th, 2003.

Contig Viewer

This graphical viewer displays contig assembly and other relatedinfo. There are many options implemented to customize the output image andtext for the researchers. Two versions have been developed with verysimilar background coding but different usages. One is an online PHPversion, the other one is a standalone Python version.
http://cgpdb.ucdavis.edu/database/chromat_viewer/CV_main.php (php version)
http://www.atgc.org/Py_ContigViewer/ (python version)

Python BLAST info viewer

It is designed to view results of BLASTX search of the set ofESTs (or contigs) against Arabidopsis predicted proteins. The viewerdisplays graphical alignments for the first three best hits (if found)from BLAST report as well as intron-exon positions for Arabidopsis proteinsequence.

xgeolocate - IP locator

It looks for the respective geographical location(s) from thenetgeo server, then it plots the result on a world map. After plotting,the result can be saved into a data output file. Next time the user candirectly plot the locations on the world map with that data file as aninput file.


This Graph9 program does clustering based on adjacency matrix.An adjacency matrix representation of a graph is a V-by-V array of Booleanvalues, with the entry in row v and column w defined to be 1 if there isan edge connecting vertex v and vertex w in the graph, and to be 0otherwise.

BLAST parser

Almost any bioinformatician wrote at least once in his/herlifetime a BLAST parser for some particular needs. Major advantages of ourparser are automatic generation of the "Matrix file" suitable forprotein/sequence clustering analysis, and generation of the "Two HitsFile" which helps to distinguish orthologs from paralogs in the case ofBLAST search of one genome against another, for example: Lettuce/SunflowerCOS candidates (Conserved Orthologs Set) web page.

Sequence Retrieval by Keywords

Blast Search Parser matches a given a keyword with the words inBLAST hit description line.If the description line contains a searchable word, a cutoff value iscompared. Blast Search Parserwill extract the contig with the largest expectation value above the cutoff value.

Though these programs are free to use, they are written underthoughtful planning and careful coding. I hope you find them useful foryour professional and maybe even personal use. If you are looking for aprogrammer to help you develop some useful software, please do nothesitate to contact me by email (birdchan@ucdavis.edu).

I am looking forward to furthering my education in the field ofComputer Science. My academic goal is to obtain a PhD in Computer Science.

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