E. BioBIKE principles

• Permits use of names familiar to the biologist
  BBL allows the user to refer to genes, proteins, replicons, and contigs by their common names:

  (PROTEINS-SIMILAR-TO p-All4312 IN PCC6803
  :: (("S6803.p-Sll1330" 2.6d-93) ("S6803.p-Slr0947" 1.2d-32) . . .
  
  (SEQUENCE-OF pSYSA)
  :: "GGCGCGCCACCGTGTACCCAGTTTCCTCGGAATGGAACGTAATGCGCTCA..."
  
  *nucleotides*
  :: ("A" "C" "G" "T")

• Names functions in a way familiar to the biologist
  

  (SEQUENCES-UPSTREAM-OF (ORTHOLOGS-OF (GENE-CALLED "glnA" IN Npun)))
  :: [sequences upstream of several glnA orthologs]
  
  (COUNT-OF *nucleotides* IN A7120.chromosome)
  :: (1878490 1323814 1328123 1883344)

• Interconverts between gene and protein as appropriate
  

  (MW-OF all4312)       [Figures you must want the molecular weight of the encoded protein]
  :: 33742
  
  (GENES-UPSTREAM-OF (ORTHOLOGS-OF p-all4312))       [Realizes that gene upstream of protein makes no sense]
  :: (#$S7942.ser1031 #$Gvi.gsr2273 #$TeBP1.tll1329 #$Cwat.Cw?1563 . . .)

• Allows and converts any reasonable data type
  The following all give the same result:

  (ORTHOLOGS-OF all4312)
  (ORTHOLOGS-OF "all4312")
  (ORTHOLOGS-OF 'all4312)
  (ORTHOLOGS-OF #$A7120.all4312)
  

• Allows input information to be single entities or lists of entities.

  (MW-OF p-NpF0001)
  :: 60335
  
  (MW-OF (ORTHOLOGS-OF p-NpF0001))
  :: (59857 60278 60366 60335 57866)

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