Impact on Bioinformatics

• A DOE ``Impossible'' query.
  Find for each gene located on a particular cytogenetic band of a particular human chromosome, as many of its non-human homologs as possible.
  
  
  
  
• Data sources involved

  source type location remarks

  GDB Sybase Baltimore flat tables SQL-based joins cytogenetic bands info

  Entrez ASN.1 Bethesda nested tables keyword and links seq and homolog info

  
  
  
  

• Implementation in Kleisli

  sybase-add (#name:"gdb", ...);
  readfile locus from "locus_cyto_location" using gdb;
  readfile eref from "object_genbank_eref" using gdb;
  
  {(#accn: g.#genbank_ref, #nonhuman-homologs: H)
  | \c <- locus, c.#chrom_num = "22",
    \g <- eref, g.#object_id = c.#locus_id,
    \H == { u
          | \u <- na-get-homolog-summary(g.#genbank_ref),
            not(u.#title string-islike "%Human%"),
            not(u.#title string-islike "%H.sapien%")},
    not (H = { })}