
                                crystalball 



Function

   Answers every drug discovery question about a sequence

Description

   Crystalball is an application invented by Scott Markel and Darryl Leon
   in their book "Sequence Analysis in a Nutshell". They put the
   description into Appendix D with the comment:

   Here's a program we're working on. When it's finished we plan to
   donate it to the EMBOSS package. It may take us a while, so be patient

   It took just 30 minutes from seeing a draft of Appendix D to sending
   Scott the ACD file and then the C source code.

   Like Scott and Darryl, we put the program into an EMBASSY package
   called "appendixd" in the hope that nobody takes it too seriously,
   although we suspect the results are more accurate than one would
   reasonably be entitled to expect.

Algorithm

   Scott and Darryl defined the ACD interface in the book, together with
   3 of the responses.

   We added the others in the same spirit.

   No attempt is made to change the output when the input sequence
   changes.

Usage

   Here is a sample session with crystalball


% crystalball -competition -rdtime -rdcost -animalstudies -clinicaltrials -fdap
roblems -fdatime -profit -everythingelse 
Answers every drug discovery question about a sequence.
Input sequence: tembl:hsfau
Output file [hsfau.crystalball]: 

   Go to the input files for this example
   Go to the output files for this example

Command line arguments

   Standard (Mandatory) qualifiers:
  [-sequence]          sequence   Sequence USA
  [-outfile]           outfile    Output file name

   Additional (Optional) qualifiers:
   -competition        boolean    Who else is working with this target?
   -rdtime             boolean    Total research and development time to bring
                                  a drug for this target to market.
   -rdcost             boolean    Total cost of our research and development
                                  effort.
   -animalstudies      boolean    What will we learn from the animal studies?
   -clinicaltrials     boolean    Detail all of the surprises we'll get from
                                  the clinical trials.
   -fdaproblems        boolean    List all of the issues the FDA will raise
                                  with our paperwork.
   -fdatime            boolean    How long will the FDA take to render a
                                  decision?
   -profit             boolean    How much will we make after the drug gets to
                                  market?

   Advanced (Unprompted) qualifiers:
   -everythingelse     boolean    Tell us everything else we'd really like to
                                  know now rather than later

   Associated qualifiers:

   "-sequence" associated qualifiers
   -sbegin1            integer    Start of the sequence to be used
   -send1              integer    End of the sequence to be used
   -sreverse1          boolean    Reverse (if DNA)
   -sask1              boolean    Ask for begin/end/reverse
   -snucleotide1       boolean    Sequence is nucleotide
   -sprotein1          boolean    Sequence is protein
   -slower1            boolean    Make lower case
   -supper1            boolean    Make upper case
   -sformat1           string     Input sequence format
   -sdbname1           string     Database name
   -sid1               string     Entryname
   -ufo1               string     UFO features
   -fformat1           string     Features format
   -fopenfile1         string     Features file name

   "-outfile" associated qualifiers
   -odirectory2        string     Output directory

   General qualifiers:
   -auto               boolean    Turn off prompts
   -stdout             boolean    Write standard output
   -filter             boolean    Read standard input, write standard output
   -options            boolean    Prompt for standard and additional values
   -debug              boolean    Write debug output to program.dbg
   -verbose            boolean    Report some/full command line options
   -help               boolean    Report command line options. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose
   -warning            boolean    Report warnings
   -error              boolean    Report errors
   -fatal              boolean    Report fatal errors
   -die                boolean    Report deaths


   Standard (Mandatory) qualifiers Allowed values Default
   [-sequence]
   (Parameter 1) Sequence USA Readable sequence Required
   [-outfile]
   (Parameter 2) Output file name Output file <sequence>.crystalball
   Additional (Optional) qualifiers Allowed values Default
   -competition Who else is working with this target? Boolean value
   Yes/No No
   -rdtime Total research and development time to bring a drug for this
   target to market. Boolean value Yes/No No
   -rdcost Total cost of our research and development effort. Boolean
   value Yes/No No
   -animalstudies What will we learn from the animal studies? Boolean
   value Yes/No No
   -clinicaltrials Detail all of the surprises we'll get from the
   clinical trials. Boolean value Yes/No No
   -fdaproblems List all of the issues the FDA will raise with our
   paperwork. Boolean value Yes/No No
   -fdatime How long will the FDA take to render a decision? Boolean
   value Yes/No No
   -profit How much will we make after the drug gets to market? Boolean
   value Yes/No No
   Advanced (Unprompted) qualifiers Allowed values Default
   -everythingelse Tell us everything else we'd really like to know now
   rather than later Boolean value Yes/No No

Input file format

   crystalball reads any normal sequence USAs.

  Input files for usage example

   'tembl:hsfau' is a sequence entry in the example nucleic acid database
   'tembl'

  Database entry: tembl:hsfau

ID   HSFAU      standard; RNA; HUM; 518 BP.
XX
AC   X65923;
XX
SV   X65923.1
XX
DT   13-MAY-1992 (Rel. 31, Created)
DT   23-SEP-1993 (Rel. 37, Last updated, Version 10)
XX
DE   H.sapiens fau mRNA
XX
KW   fau gene.
XX
OS   Homo sapiens (human)
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia
;
OC   Eutheria; Primates; Catarrhini; Hominidae; Homo.
XX
RN   [1]
RP   1-518
RA   Michiels L.M.R.;
RT   ;
RL   Submitted (29-APR-1992) to the EMBL/GenBank/DDBJ databases.
RL   L.M.R. Michiels, University of Antwerp, Dept of Biochemistry,
RL   Universiteisplein 1, 2610 Wilrijk, BELGIUM
XX
RN   [2]
RP   1-518
RX   MEDLINE; 93368957.
RA   Michiels L., Van der Rauwelaert E., Van Hasselt F., Kas K., Merregaert J.;
RT   " fau cDNA encodes a ubiquitin-like-S30 fusion protein and is expressed as
RT   an antisense sequences in the Finkel-Biskis-Reilly murine sarcoma virus";
RL   Oncogene 8:2537-2546(1993).
XX
DR   SWISS-PROT; P35544; UBIM_HUMAN.
DR   SWISS-PROT; Q05472; RS30_HUMAN.
XX
FH   Key             Location/Qualifiers
FH
FT   source          1..518
FT                   /chromosome="11q"
FT                   /db_xref="taxon:9606"
FT                   /organism="Homo sapiens"
FT                   /tissue_type="placenta"
FT                   /clone_lib="cDNA"
FT                   /clone="pUIA 631"
FT                   /map="13"
FT   misc_feature    57..278
FT                   /note="ubiquitin like part"
FT   CDS             57..458
FT                   /db_xref="SWISS-PROT:P35544"
FT                   /db_xref="SWISS-PROT:Q05472"
FT                   /gene="fau"
FT                   /protein_id="CAA46716.1"
FT                   /translation="MQLFVRAQELHTFEVTGQETVAQIKAHVASLEGIAPEDQVVLLA
G
FT                   APLEDEATLGQCGVEALTTLEVAGRMLGGKVHGSLARAGKVRGQTPKVAKQEKKKKKT
G
FT                   RAKRRMQYNRRFVNVVPTFGKKKGPNANS"
FT   misc_feature    98..102
FT                   /note="nucleolar localization signal"
FT   misc_feature    279..458
FT                   /note="S30 part"
FT   polyA_signal    484..489
FT   polyA_site      509
XX
SQ   Sequence 518 BP; 125 A; 139 C; 148 G; 106 T; 0 other;
     ttcctctttc tcgactccat cttcgcggta gctgggaccg ccgttcagtc gccaatatgc        6
0
     agctctttgt ccgcgcccag gagctacaca ccttcgaggt gaccggccag gaaacggtcg       12
0
     cccagatcaa ggctcatgta gcctcactgg agggcattgc cccggaagat caagtcgtgc       18
0
     tcctggcagg cgcgcccctg gaggatgagg ccactctggg ccagtgcggg gtggaggccc       24
0
     tgactaccct ggaagtagca ggccgcatgc ttggaggtaa agttcatggt tccctggccc       30
0
     gtgctggaaa agtgagaggt cagactccta aggtggccaa acaggagaag aagaagaaga       36
0
     agacaggtcg ggctaagcgg cggatgcagt acaaccggcg ctttgtcaac gttgtgccca       42
0
     cctttggcaa gaagaagggc cccaatgcca actcttaagt cttttgtaat tctggctttc       48
0
     tctaataaaa aagccactta gttcagtcaa aaaaaaaa                               51
8
//

Output file format

   crystalball outputs a plain text file with a one-line response to each
   of the input options.

  Output files for usage example

  File: hsfau.crystalball

Drug discovery development time: 10-15 years
Drug discovery development cost: $800 million
Animal studies results: 'Animals are not like humans'
Clinical trials surprises: Unfortunately, not another Viagra
FDA issues: List not yet complete
FDA time to decision: Waiting .........
Profit: Not nearly as much as you'd like!
The competition: Every EMBOSS user now knows as much as you!
Everything else: Trust me, you really don't want to know just now!

Data files

Notes

   None.

References

   Markel S and Leon D (2003) "Sequence Analysis in a Nutshell" O'Reilly
   and Associates Inc. See "Appendix D"

Warnings

   None.

Diagnostic Error Messages

   None.

Exit status

   It always exits with status 0.

Known bugs

   None.

See also

   Program name            Description
   myseq        Demonstration of sequence reading
   mytest       Demonstration of sequence reading

Author(s)

   Peter Rice (pmr © ebi.ac.uk)
   Informatics Division, European Bioinformatics Institute, Wellcome
   Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK

History

   Written (Feb 2003) - Peter Rice.

Target users

   This program is intended to be used by everyone and everything, from
   naive users to embedded scripts.

Comments
