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Biological sequence analysis tools

Project description

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.

Project details


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