From: toms@fcs260c2.ncifcrf.gov (Tom Schneider)
Subject: Re: Apologies for Disappearing Division
Organization: Frederick Cancer Research and Development Center
Date: Tue, 22 Dec 1992 02:15:41 GMT

In article <BzMtvt.C8n@usenet.ucs.indiana.edu>
gilbertd@sunflower.bio.indiana.edu (Don Gilbert) writes:
|In article <1992Dec21.132627.17314@news.miami.edu>
|kramer@news.miami.edu (Jack Kramer) writes:
|>Wearing a biologist hat, what I would like to really see is:
|>
|>"Genbank, send me the 16S rRNA gene for E. coli"
|
|We are getting close to that now.  I just tried your question on
|the Gopherized copy of Genbank here at IUBio, with these results:
|
|  Search GenBank: Genbank, send me the 16S rRNA gene for E. coli
|
|1.  K01983 Anacystis nidulans partial 16S rRNA, Ile-tRNA and Ala-tRNA genes;.
|2.  X12420 Escherichia coli DNA for 16S-23S intergenic region..
|3.  M29364 E.coli ATP-dependent protease binding subunit (clpB) gene, compl.
|4.  J01694 E.coli rRNA operon (rrnA) coding for 16S rRNA, promoter region..
|5.  J01695 E.coli rRNA operon (rrnB) coding for Glu-tRNA-2, 5S, 16S and 23S.
|6.  M10739 E.coli rrnC operon promoter region and 16S rRNA gene 5'end..
|7.  J01692 E.coli rRNA operon (rrnD*) gene coding for 16S rRNA, promoter.
|8.  J01702 E.coli rRNA operon (rrnD*) coding for ile-tRNA-1, ala-tRNA-1B and.
|9.  J01697 E.coli rRNA operon (rrnE) coding for 16S rRNA, promoter..
|10. J01700 E.coli rRNA operon (rrnx: rrnG or rrnF), coding for 16S rRNA,.
|11. K00763 E.coli rRNA operon (rrnX), coding for ile-tRNA-1,ala-tRNA-1B and.
|12. V00330 E. coli gene rrnA for 16S ribosomal RNA.
|13. K01056 E.coli 16s rrna gene (partial)..
|14. K01057 E.coli 16s rrna (3' end) & ile-trna-1 genes..
|15. M58020 Mycobacterium leprae 16S rRNA gene, 5' end..
|16. S39788 16S rRNA [Escherichia coli, subsurface soil, cluster III, rRNA.
|17. M87484 Tropheryma whippelii homologue to Escherichia coli 16S rRNA (from.
|18. X01339 Bombyx mori 18S rRNA gene, 3' end..
|19. V01390 Trypanosoma brucei kinetoplast DNA maxicircle fragment encoding .
|20. X12890 E.gracilis rrnC operon 16S, 23S and 5S rRNA, tRNA-Ile and tRNA-A.
|21. V00653 A. nidulans mitochondrial genes for 16S rRNA and tRNA-Tyr (conta.
|22. J01390 a.nidulans mt dna between h2/h5 & bh2/b2 junctions. genes for.
|23. Z00028 Zea mays chloroplast rRNA-operon.
|24. M59073 Campylobacter coli 16S ribosomal RNA..
|25. L04312 Campylobacter coli, complete 16S ribosomal RNA..
|26. M25458 E.coli 23S rRNA..
|27. J01859 E.coli 16S ribosomal RNA..
|28. M35308 E.coli 16S rRNA fragment..
|29. M35309 E.coli 16S rRNA fragment..
|30. M25588 E.coli 16S rRNA..
|31. M25051 E.coli T1 ribonuclease sensitive 16S rRNA region, segment 1..
|32. M25052 E.coli T1 ribonuclease sensitive 16S rRNA region, segment 2..
|...
|
|This searching software (WAIS) is designed to handle english language queries
|such as yours, and it generally works pretty well.

|You still have to weed out the ones you don't want from this selection.

Right.  You get splattered with garbage.  Fragments.  Irrelevant species.
Overlaps which are inconsistent.  Errors.  Huge numbers of similar sequences
(ie things like immunoglobulins that are sequenced more than other genes and so
they mess up careful statistics).  So you have to wade through all that to get
what you want.  Every time.  And anybody else in the world who wants the 7 16S
sequences HAS TO REPEAT THAT EFFORT.  Oh yes, the ACCESSION names will in some
cases give you huge entries containing the stuff you want.  So you have to
dissect each one.  (Tough if you don't have Delila up and running, easier if
you do.)  We do this in our projects, but it's long hard work.  Then they alter
the LOCUS or update the ACCESSION number and within half a year to a year the
Delila instructions are trashed.  One basically has to start again from
scratch.  GIGO: Garbage In Garbage Out.  The massiveness of the problem is
unbelievable.  Ask for human splice sites!

Oh yes, you won't get everything either because not everything is recorded
in the features tables.  So to do a serious job, you also have to dig
around in the PHYSICAL library for hours.  For splice junctions make that
years.  Whoops, I forgot.  It took us about a year to analyze the database.
(WITHOUT LOOKING AT MOST OF THE ORIGINAL PAPERS).  But the database doubles
every 1.5 years.  So by the time one is done the job has doubled.

Ever hear of Sisyphus?  It's exactly the same.  We analyzed nearly 1800 human
splice junctions.  The database changed.  We are now again at the bottom of the
splice junction hill.  But my student has left and the number is now 6000
junctions.  As I said, I estimate 2000 of those are errors.  Some of the errors
have already been confirmed.

Wouldn't it be nice if I COULD write the Delila II instructions and be even 90%
sure that they were stable?  I could just email you the instruction set and you
could them use them directly or you could delete and modify for your own
purposes.  We could have libraries of INSTRUCTIONS - whenever somebody studied
something the instructions for obtaining their data could be kept in an
archive, available for anybody to repeat.  When I (finally!) publish an
analysis, the instructions are in my archive.  But you won't be able to re
extract them from the big databases because of their unstable names, so I have
to supply the books also (see files in ncifcrf.gov/pub/delila/splice*).

  Tom "Cassandra-points-at-Sisyphus, Delila weeps" Schneider
  National Cancer Institute
  Laboratory of Mathematical Biology
  Frederick, Maryland  21702-1201
  toms@ncifcrf.gov