This page focuses on the project results. If you are looking for details of PyMood usage please refer to our bacterial project example.
1. Identification of the Arabidopsis proteins with highly similar homologs in the other three species
2. Identification of Arabidopsis "specific" proteins
3. Identification of Arabidopsis genes, which are only present in one or two of the other species
Materials and Methods
The entire project was performed on a laptop running Windows XP with the following system setup:
RAM: 256 MB
Processor: 1GHz Athlon
Graphics Card: S3 graphics Twister K Compaq with 16 megabytes memory
Software used: PyMood, WordPad, MS Excel 2000, Netscape 7, MSIE 6
1. Predicted protein sequence files were downloaded in a FASTA format, from publicly available sources.
2. Using the "Combine" function of the PyMood Blast Launcher all S. cerevisiae protein files were combined into one FASTA file, S_cerevisiae.faa, and all C. elegans files were combined into C_elegans.faa file.
3. PyMood BLAST Launcher was run between the Arabidopsis protein database and the three target protein databases, S. cerevisiae, H. sapiens, and C. elegans. These can be downloaded from our blastp outputs page.
The limit of our expectation cutoff in the PyMood BLAST Launcher was set to e-8.
4. Using the PyMood Data File Setup window an Ath_sc_hs_ce.rgb file was created to represent the homology between Arabidopsis and yeast proteins on the red axis, the homology between Arabidopsis and human on the green axis, and the homology between Arabidopsis and worm on the blue axis.
5. The Ath_sc_hs_ce.rgb file was visualized in the PyMood 2D and 3D Viewers. The relevant data was extracted and saved as html or text files.
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