grimoire 0.0.2

Biological sequence analysis tools

grimoire

The grimoire pacakage contains libraries and scripts for Biological sequence analysis.

Disclaimer

The current developent is highly volatile and not ready for public consumption.

Design Considerations

The code is designed with the folllowing analyses in mind:

• Gene structure prediction using hidden Markov models and variants
• Genome annotation quality control
• Structure-function relationships in sequences (e.g. IME)

Programs

Program names are themed after spell names from the classic RPG "Wizardry: Proving Grounds of the Mad Overlord."

Name	Meaning	Function
calfo	x-ray	genome annotation reporter
kandi	locate	genome annotation viewer
haman	change	genome slicer
milwa	light	hmm buider
dumapic	clarity	hmm grapher
halito	fire	basic hmm decoder
mahalito	big fire	2-pass gene decoder
morlis	fear	annotation comparer (simple)
mogref	iron	sequence generator
mamorlis	great fear	(planned complex annotation comparer)
mahaman	change	(planned multi-genome slicer)
malor	apport	(planned genome lifter)
lahalito	torch	(planned full genome decoder)
tiltowait	explosion	(planned multi-genome decoder)
zilwan	dispel	(planned profile/alignment decoder)
latumapic	identify	(planned region-ifier)

Contributors

• Ian Korf (iankorf)
• Hannah Lyman (hslyman)
• Alex Kramer (aklreaxmer)
• Qijia Liu (joyliu-q)
• Jack Yu (Angraygs)

Acknowledgements

Thanks to M. O. Trebor and E. W. Werdna for inspiration.