Genomics Data Visualization Software
» (PyMood is discontinued, this website is an archive) «
PyMood is a desktop application for visualizing genomic data.
It is used to analyze and display relations between complete
genomic fragments, proteins, ESTs, full length cDNAs, and virtually any sets of sequences. The program is also used to visualize and analyze expression data.
The user-friendly environment of PyMood enables biologists at all levels of bioinformatics knowledge to perform:
Here are some example questions that can be answered using PyMood:
- running local BLAST on a desktop
- processing of FastA files; removing and masking undesired sequences
- modification of FastA files: combining, splitting of files and sequences, creation of non-redundant sets, etc.
- post-processing of BLAST outputs (BLAST parser is built into the PyMood BLAST
- visual browsing in 2D and 3D environments through BLAST results or expression data points
- retrieval of data and alignments from the visual interfaces using comprehensive querying system built into the PyMood 3D Viewer
- data retrieval from remote databases
- auto-construction of web pages with browsable images from data outputs
- What are the genes specific to my library (or any other set of sequences)?
- What are the sequences common to all tested sets of genes or proteins?
- What are the genes common only to some sets, but absent in others?
- Are there membrane (or any other word here) proteins highly conservative between some sets of genes, but absent in the others?
- What are the genes from a particular species which have equally distant homologs in other species?
- Are there any tissue specific kinases (or any other definition here)?
- Which genes are the housekeeping genes?
"PyMood has allowed us to do research that we just couldn't have done before"
John Yoder, Professor and Chair of the Dept. of Veg. Crops at UC Davis
"The BLAST parser and tools for data set manipulation are also extremely useful for incorporating into other, independent
Ed DeLong, Professor, MIT