Home

Python

No EOF(), the Python way

July 7, 2008 - 17:09 — forrest

by Forrest Sheng Bao http://fsbao.net

Today, I was writing a program and gonna to find a function to detect whether EOF, the end of file marker, was reached. But I failed. Not such function in file I/O of Python. Then I did some googling and realized we don't need an EOF detection function. Take a look at this: http://groups.google.com/group/comp.lang.python/browse_thread/thread/ed25388487b3ac7b

Searching phased siRNAs from mapping result over genomes in linear (O(n)) time complexity

July 5, 2008 - 18:56 — forrest

by Forrest Sheng Bao http://fsbao.net

In bioinformatics, we prefer constant or linear algorithms. The reason is obvious. But, sometimes, something strange just happened in some papers.

In 2006, Ho-Ming Chen, Yi-Hang Li and Shu-Hsing Wu published a paper on PNAS, "Bioinformatic prediction and experimental validation of a microRNA-directed tandem trans-acting siRNA cascade in Arabidopsis", http://www.pnas.org/content/104/9/3318.abstract.

Truncating siRNAs by 5' and 3' adapters and categorizing them

March 7, 2008 - 20:13 — forrest

by Forrest Sheng Bao http://fsbao.net

Some genes in DNA sequences are very short, for example 15 bases. They are too short to sequence. So, we can add some adapters at 5' and 3' to extend it to 34 bases. Besides, we have a huge pool of sequences from different sources and we mixed them up for sequencing. So we can also use the adapter as an indicator to mark the source of the gene.

PyWavelets and pywfdb library for biomedical time series analysis

March 1, 2008 - 19:51 — forrest

by Forrest Sheng Bao http://fsbao.net

I am so excited today that I have found a very cool Python library for doing wavelet decomposition, the PyWavelets. It is developed by Filip Wasilewski

Plotting in matplotlib/pylab

February 29, 2008 - 01:37 — forrest

by Forrest Sheng Bao http://fsbao.net

I like Python, the simple but elegant syntax. I can't love any other programming languages more than Python. So I prefer to do my scientific computing in Python. I am very happy to find Numpy/SciPy package. matplotlib/pylab makes it possible for me to visualize my results. Neat!

Here is my first plotting script using matplotlib/pylab:

Python implementation of Nussinov Folding Algorithm for RNA Secondary Structure Prediction

November 29, 2007 - 20:05 — forrest 
#This software is a free software. 
#Thus, it is licensed under GNU General Public License.
#Python implementation to Nussinov Folding Algorithm 
#for Homework 7 of Bioinformatics class.
#Forrest Bao, Nov.

Python implementation of Feng-Doolittle Algorithm for Multiple Sequence Alignment

November 17, 2007 - 11:23 — forrest 
#This software is a free software. 
#Thus, it is licensed under GNU General Public License.
#Python implementation to Fen-Doolittle Algorithm
#for Homework 6 of Bioinformatics class.
#Forrest Bao, Nov.

Smith-Waterman Algorithm in Python

September 25, 2007 - 00:04 — forrest

by Forrest Sheng Bao http://fsbao.net

Syndicate content