crystalball |
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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.
We added the others in the same spirit.
No attempt is made to change the output when the input sequence changes.
% 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]: |
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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 |
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 // |
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! |
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Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.
Written (Feb 2003) - Peter Rice.