• Returns the genetic context surrounding a coordinate in a replicon or contig
• IN contig-or-replicon is mandatory. The name of an organism may also be used, but only if the genome contains only one sequence (i.e. no plasmids)
• At present TO and LENGTH are ignored (will be used eventually to permit context of DNA segments)
• CONTEXT-OF considers the following cases:
     CASE 1: Coordinate lies within a gene
        Returns ("I" gene-frame NIL distance-from-start-of-gene
               distance-from-end-of-gene direction-of-gene)
     CASE 2: Coordinate lies between parallel genes
        Returns ("P" left-gene-frame right-gene-frame distance-from-downstream-end
               distance-from-upstream-end direction-of-genes)
     CASE 3: Coordinate lies between convergent genes
        Returns ("C" left-gene-frame right-gene-frame distance-from-left-gene
               distance-from-right-gene direction-of-left-gene)
     CASE 4: Coordinate lies between divergent genes
        Returns ("D" left-gene-frame right-gene-frame distance-from-left-gene
               distance-from-right-gene direction-of-left-gene)

Example:
  (CONTEXT-OF 423440 IN Npun.chromosome)
  :: ("I" #$Npun.NpF0337 NIL 363 1325 :F)

[Result Coordinate 423440 in the chromosome of Nostoc punctiforme lies within gene NpF0337 (on the forward strand), 363 nt from the beginning and 1325 from the end]

Example: Find all "consensus" NtcA-binding sites in the Anabaena PCC 7120 chromosome
  (ASSIGN NtcA-site "GTA.{8}TAC.{20,24}TA...T")
:: "GTA.{8}TAC.{20,24}TA...T"

  (PATTERN-MATCH-ALL NtcA-site (SEQUENCE-OF A7120.chromosome))
:: ((39214 39258) (122626 122666) (161182 161223) (244923 244965)
  (335765 335805) (362991 363035) (382010 382051) (382802 382842)
  (391102 391144) (464318 464358) (512035 512075) (576956 576997)
  (617268 617308) (677480 677520) (697989 698032) (704168 704210)
  (131 more)

  (LOOP FOR item IN *
    COLLECT (FIRST item))
:: (39214 122626 161182 244923 335765 362991 382010 382802 391102 464318
    512035 576956 617268 677480 697989 704168 755407 784153 912152 920044
    922446 962926 999432 1028862 1063997 1087868 1128640 1149492 1156629
    ...
  (CONTEXT-OF * IN A7120.chromosome)
  :: (("D" #$A7120.all0037 #$A7120.alr0038 233 643 :B)
    ("I" #$A7120.all0121 NIL 475 949 :B)
    ("I" #$A7120.all0156 NIL 122 399 :B)
    ("I" #$A7120.asr0229 NIL 69 155 :F)
    ("D" #$A7120.asl0294 #$A7120.alr0295 410 84 :B)
    ("I" #$A7120.all0320 NIL 606 269 :B)
    ("I" #$A7120.alr0331 NIL 875 1410 :F)
    ("I" #$A7120.alr0331 NIL 1667 618 :F)
    ("I" #$A7120.all0341 NIL 615 257 :B)
    ("I" #$A7120.all0395 NIL 1260 356 :B)
    ...)

          [The great majority of such sites lie within genes and are not likely to be functional]