crystalball

 

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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 -fdaproblems -fdatime -profit -everythingelse 
Answers every drug discovery question about a sequence.
Input sequence: tembl:x65923
Output file [x65923.crystalball]:

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

Command line arguments 

Answers every drug discovery question about a sequence.
Version: EMBOSS:6.4.0.0

   Standard (Mandatory) qualifiers:
  [-sequence]          sequence   Sequence filename and optional format, or
                                  reference (input USA)
  [-outfile]           outfile    [*.crystalball] 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 first file to standard output
   -filter             boolean    Read first file from standard input, write
                                  first file to 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 and exit. 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 dying program messages
   -version            boolean    Report version number and exit

Qualifier Type Description Allowed values Default
Standard (Mandatory) qualifiers
[-sequence]
(Parameter 1)		 sequence Sequence filename and optional format, or reference (input USA) Readable sequence Required
[-outfile]
(Parameter 2)		 outfile Output file name Output file <*>.crystalball
Additional (Optional) qualifiers
-competition boolean Who else is working with this target? Boolean value Yes/No No
-rdtime boolean Total research and development time to bring a drug for this target to market. Boolean value Yes/No No
-rdcost boolean Total cost of our research and development effort. Boolean value Yes/No No
-animalstudies boolean What will we learn from the animal studies? Boolean value Yes/No No
-clinicaltrials boolean Detail all of the surprises we'll get from the clinical trials. Boolean value Yes/No No
-fdaproblems boolean List all of the issues the FDA will raise with our paperwork. Boolean value Yes/No No
-fdatime boolean How long will the FDA take to render a decision? Boolean value Yes/No No
-profit boolean How much will we make after the drug gets to market? Boolean value Yes/No No
Advanced (Unprompted) qualifiers
-everythingelse boolean Tell us everything else we'd really like to know now rather than later Boolean value Yes/No No
Associated qualifiers
"-sequence" associated sequence qualifiers
-sbegin1
-sbegin_sequence		 integer Start of the sequence to be used Any integer value 0
-send1
-send_sequence		 integer End of the sequence to be used Any integer value 0
-sreverse1
-sreverse_sequence		 boolean Reverse (if DNA) Boolean value Yes/No N
-sask1
-sask_sequence		 boolean Ask for begin/end/reverse Boolean value Yes/No N
-snucleotide1
-snucleotide_sequence		 boolean Sequence is nucleotide Boolean value Yes/No N
-sprotein1
-sprotein_sequence		 boolean Sequence is protein Boolean value Yes/No N
-slower1
-slower_sequence		 boolean Make lower case Boolean value Yes/No N
-supper1
-supper_sequence		 boolean Make upper case Boolean value Yes/No N
-sformat1
-sformat_sequence		 string Input sequence format Any string  
-sdbname1
-sdbname_sequence		 string Database name Any string  
-sid1
-sid_sequence		 string Entryname Any string  
-ufo1
-ufo_sequence		 string UFO features Any string  
-fformat1
-fformat_sequence		 string Features format Any string  
-fopenfile1
-fopenfile_sequence		 string Features file name Any string  
"-outfile" associated outfile qualifiers
-odirectory2
-odirectory_outfile		 string Output directory Any string  
General qualifiers
-auto boolean Turn off prompts Boolean value Yes/No N
-stdout boolean Write first file to standard output Boolean value Yes/No N
-filter boolean Read first file from standard input, write first file to standard output Boolean value Yes/No N
-options boolean Prompt for standard and additional values Boolean value Yes/No N
-debug boolean Write debug output to program.dbg Boolean value Yes/No N
-verbose boolean Report some/full command line options Boolean value Yes/No Y
-help boolean Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose Boolean value Yes/No N
-warning boolean Report warnings Boolean value Yes/No Y
-error boolean Report errors Boolean value Yes/No Y
-fatal boolean Report fatal errors Boolean value Yes/No Y
-die boolean Report dying program messages Boolean value Yes/No Y
-version boolean Report version number and exit Boolean value Yes/No N

Input file format

crystalball reads any normal sequence USAs.

Input files for usage example

'tembl:x65923' is a sequence entry in the example nucleic acid database 'tembl'

Database entry: tembl:x65923

ID   X65923; SV 1; linear; mRNA; STD; HUM; 518 BP.
XX
AC   X65923;
XX
DT   13-MAY-1992 (Rel. 31, Created)
DT   18-APR-2005 (Rel. 83, Last updated, Version 11)
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; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae;
OC   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   PUBMED; 8395683.
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 sequence in the Finkel-Biskis-Reilly murine sarcoma virus";
RL   Oncogene 8(9):2537-2546(1993).
XX
DR   H-InvDB; HIT000322806.
XX
FH   Key             Location/Qualifiers
FH
FT   source          1..518
FT                   /organism="Homo sapiens"
FT                   /chromosome="11q"
FT                   /map="13"
FT                   /mol_type="mRNA"
FT                   /clone_lib="cDNA"
FT                   /clone="pUIA 631"
FT                   /tissue_type="placenta"
FT                   /db_xref="taxon:9606"
FT   misc_feature    57..278
FT                   /note="ubiquitin like part"
FT   CDS             57..458
FT                   /gene="fau"
FT                   /db_xref="GDB:135476"
FT                   /db_xref="GOA:P35544"
FT                   /db_xref="GOA:P62861"
FT                   /db_xref="HGNC:3597"
FT                   /db_xref="InterPro:IPR000626"
FT                   /db_xref="InterPro:IPR006846"
FT                   /db_xref="InterPro:IPR019954"
FT                   /db_xref="InterPro:IPR019955"
FT                   /db_xref="InterPro:IPR019956"
FT                   /db_xref="UniProtKB/Swiss-Prot:P35544"
FT                   /db_xref="UniProtKB/Swiss-Prot:P62861"
FT                   /protein_id="CAA46716.1"
FT                   /translation="MQLFVRAQELHTFEVTGQETVAQIKAHVASLEGIAPEDQVVLLAG
FT                   APLEDEATLGQCGVEALTTLEVAGRMLGGKVHGSLARAGKVRGQTPKVAKQEKKKKKTG
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        60
     agctctttgt ccgcgcccag gagctacaca ccttcgaggt gaccggccag gaaacggtcg       120
     cccagatcaa ggctcatgta gcctcactgg agggcattgc cccggaagat caagtcgtgc       180
     tcctggcagg cgcgcccctg gaggatgagg ccactctggg ccagtgcggg gtggaggccc       240
     tgactaccct ggaagtagca ggccgcatgc ttggaggtaa agttcatggt tccctggccc       300
     gtgctggaaa agtgagaggt cagactccta aggtggccaa acaggagaag aagaagaaga       360
     agacaggtcg ggctaagcgg cggatgcagt acaaccggcg ctttgtcaac gttgtgccca       420
     cctttggcaa gaagaagggc cccaatgcca actcttaagt cttttgtaat tctggctttc       480
     tctaataaaa aagccactta gttcagtcaa aaaaaaaa                               518
//

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: x65923.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

Author(s)

Peter Rice
European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK

Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.

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