Talk:Protein coding sequences

Revision as of 02:47, 21 January 2009 by Rshetty (Talk | contribs)

  • BBa_J31004 - change the vector of this part
  • BBa_Y00029 - remove the prefix and suffix
  • Rename chromatinremodeling to chromatin

Questions

  • How do we want to indicate relationships between parts? - i.e. protein coding sequences and generators, transcriptional regulators and cognate promoters, similar versions of protein coding sequences,

Categories

Part level function

  • //cds/reporter
    • //cds/reporter/fluorescentprotein
    • //cds/reporter/color
    • //cds/reporter/luciferase
  • //cds/selectionmarker/antibioticresistance
  • //cds/enzyme
    • //cds/enzyme/selectionmarker/antibioticresistance (//protein/enzyme/antibiotic_resistance)
    • //cds/enzyme/recombinase (//protein/enzyme/dna_excision_integration)
    • //cds/enzyme/biosynthesis/odorant (//protein/enzyme/smell)
    • //cds/enzyme/biosynthesis/AHL (//protein/enzyme/hsl_synthesis) --> synthases?
    • //cds/enzyme/protease
    • //cds/enzyme/degradation/AHL --> lyases?
    • //cds/enzyme/methylation --> should be split into methylases, demethylases
    • //cds/enzyme/phosphorylation --> should be split into phosphorylases, kinases, and phosphatases
  • //cds/transcriptionalregulator (//protein/repact/uncategorized)
    • //cds/transcriptionalregulator/activator
    • //cds/transcriptionalregulator/repressor
  • //cds/membrane
    • //cds/membrane/receptor
    • //cds/membrane/transporter
    • //cds/membrane/channel
    • //cds/membrane/pump
    • //cds/membrane/binding
    • //cds/membrane/surfacedisplay
  • //cds/binding
    • //cds/binding/DNA
    • //cds/binging/lead
  • //cds/chromatin

Device level function

  • //function/motility
  • //function/conjugation
  • //function/sensor
    • //function/sensor/light
    • //function/sensor/lead
    • //function/sensor/odor
  • //function/odor

Parameters

The following parameters can be auto-selected by the computer.

  • Completeness <-- need a better name here
    • Full-length
      • begins with ATG/GTG and ends with TAA/TGA/TAG
      • begins with TTA/TCA/CTA and ends with CAT/CAC
    • N-terminus
      • begins with ATG/GTG or ends with TAA/TGA/TAG
    • C-terminus
      • begins with TTA/TCA/CTA or ends with CAT/CAC
    • Fusion
    • Domain
      • has neither an ATG/GTG nor a TAA/TGA/TAG
  • Direction
    • Forward
      • begins with ATG/GTG or ends with TAA/TGA/TAG
    • Reverse
      • begins with TTA/TCA/CTA or ends with CAT/CAC
  • Degradation tag
    • probably ought to be able to auto-detect and annotate the different degradation tags as well. I'll compile the different sequences and tag names. May want to somehow tie this with the Protein tags and modifiers parts.
  • Signal sequences
    • do the same with N-terminal tags?

Columns

  • all protein coding sequences
    • Protein
    • Description
    • Direction (auto-generated)
    • Completeness (auto-generated)
    • Tags (auto-generated based on sequence search)
    • SwissProt
    • KEGG
    • Length
  • all enzymes
    • EC number
    • substrate
    • product
  • fluorescent_reporter_protein_coding_sequences
    • excitation
    • emission
    • color
  • luminescent_reporter_protein_coding_sequences
  • color_reporter_protein_coding_sequences
    • color
  • antibiotic_resistance_marker
    • antibiotic
  • recombination_protein_coding_sequences
    • recombination site
  • transcriptional_regulators
    • operator site sequence
    • ligand