001
002
003 import dbd
004
005 cellhead()
006
007 print "Introduction"
008
009 cellbody()
010
011 print """
012 <p class="text_justify">DBD is a database of predicted transcription factors in completely sequenced genomes.<br>
013 The predicted transcription factors all contain assignments to
014 sequence specific DNA-binding domain families.
015 The predictions are based on domain assignments from the
016 <a href="http://supfam.org">SUPERFAMILY</a> and
017 <a href="http://www.sanger.ac.uk/Software/Pfam/">Pfam</a>
018 hidden Markov model libraries.
019 Benchmarks of our transcription factor predictions show they are
020 accurate and have wide coverage on a genomic scale. <br>
021 The DBD consists of predicted transcription factor repertoires for """
022
023 [genome_count] = dbd.get_individual_genome_count()
024
025 print '''%s''' %genome_count
026
027 print """ completely sequenced genomes.<br>
028
029 From this website you can:
030 <ul>
031 <li><a href="%(url)s?Browse">Browse genome-wide</a> transcription factor repertoire predictions</li>
032 <li>View manually curated list of sequence specific <a href="%(url)s?Domain+domain:all"> DNA binding domain families</a></li>
033 <li><a href="%(url)s?Search">Search</a> for a sequence id, domain family or submit a protein sequence</li>
034 </ul>
035
036 See the <a href="%(url)s?About">About</a> section and the recent publication for further details.<br>
037
038
039 <fieldset>
040
041 <h2 class="citation_title">Genomic repertoires of DNA-binding transcription factors across the tree of life</h2>
042
043 <a href='http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Search&itool=pubmed_AbstractPlus&term=%%22Charoensawan+V%%22%%5BAuthor%%5D' target="blank">Varodom Charoensawan</a>,
044 <a href='http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Search&itool=pubmed_AbstractPlus&term=%%22Wilson+D%%22%%5BAuthor%%5D' target="blank">Derek Wilson</a>,
045 <a href='http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Search&itool=pubmed_AbstractPlus&term=%%22Teichmann+SA%%22%%5BAuthor%%5D' target="blank">Sarah A. Teichmann</a>
046 <br>
047
048 <em>Nucleic Acids Research</em> 2010 Nov;38(21):7364-77. doi: 10.1093/nar/gkq617. Epub 2010 Jul 30. Review.
049 <br>
050
051 <b>Abstract</b> [ <a href="http://www.ncbi.nlm.nih.gov/pubmed/20675356"><img src=Images/pubmed.gif border=0 alt=PubMed></a> ]
052 <b>Full text</b> [ <a href="http://nar.oxfordjournals.org/content/38/21/7364.long">HTML</a> ·
053 <a href="http://nar.oxfordjournals.org/content/38/21/7364.full.pdf"><img alt=PDF title=PDF src=Images/pdf.gif border=0></a> ]
054
055 <br>
056
057 <h2 class="citation_title">Lineage-specific expansion of DNA-binding transcription factor families</h2>
058
059 <a href='http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Search&itool=pubmed_AbstractPlus&term=%%22Charoensawan+V%%22%%5BAuthor%%5D' target="blank">Varodom Charoensawan</a>,
060 <a href='http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Search&itool=pubmed_AbstractPlus&term=%%22Wilson+D%%22%%5BAuthor%%5D' target="blank">Derek Wilson</a>,
061 <a href='http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Search&itool=pubmed_AbstractPlus&term=%%22Teichmann+SA%%22%%5BAuthor%%5D' target="blank">Sarah A. Teichmann</a>
062 <br>
063
064 <em>Trends Genetics</em> 2010 Sep;26(9):388-93. doi: 10.1016/j.tig.2010.06.004. Epub 2010 Jul 31.
065 <br>
066
067 <b>Abstract</b> [ <a href="http://www.ncbi.nlm.nih.gov/pubmed/20675012"><img src=Images/pubmed.gif border=0 alt=PubMed></a> ]
068 <b>Full text</b> [ <a href="http://www.sciencedirect.com/science/article/pii/S0168952510001277">HTML</a> ·
069 <a href="http://pdn.sciencedirect.com/science?_ob=MiamiImageURL&_cid=271227&_user=776054&_pii=S0168952510001277&_check=y&_origin=article&_zone=toolbar&_coverDate=2010--30&view=c&originContentFamily=serial&wchp=dGLbVlS-zSkWA&md5=085f289edbdeeb5360631a1a4060e1ad&pid=1-s2.0-S0168952510001277-main.pdf"><img alt=PDF title=PDF src=Images/pdf.gif border=0></a> ]
070
071 <br>
072
073 <h2 class="citation_title">DBD - taxonomically broad transcription factor predictions: new content and functionality</h2>
074
075 <a href='http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Search&itool=pubmed_AbstractPlus&term=%%22Wilson+D%%22%%5BAuthor%%5D' target="blank">Derek Wilson</a>,
076 <a href='http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Search&itool=pubmed_AbstractPlus&term=%%22Charoensawan+V%%22%%5BAuthor%%5D' target="blank">Varodom Charoensawan</a>,
077 <a href='http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Search&itool=pubmed_AbstractPlus&term=%%22Kummerfeld+SK%%22%%5BAuthor%%5D' target="blank">Sarah K. Kummerfeld</a>,
078 <a href='http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Search&itool=pubmed_AbstractPlus&term=%%22Teichmann+SA%%22%%5BAuthor%%5D' target="blank">Sarah A. Teichmann</a>
079 <br>
080
081 <em>Nucleic Acids Research</em> 2008 36(Database issue):D88-D92; doi:10.1093/nar/gkm964
082 <br>
083
084 <b>Abstract</b> [ <a href="http://www.ncbi.nlm.nih.gov/pubmed/18073188"><img src=Images/pubmed.gif border=0 alt=PubMed></a> ]
085 <b>Full text</b> [ <a href="http://nar.oxfordjournals.org/cgi/content/full/36/suppl_1/D88">HTML</a> ·
086 <a href="http://nar.oxfordjournals.org/cgi/reprint/36/suppl_1/D88.pdf"><img alt=PDF title=PDF src=Images/pdf.gif border=0></a> ]
087
088 <br>
089 <b>Download citation</b>
090 [ <a href="./articles/nar2008.ris">RIS (for EndNote, Reference Manager, ProCite)</a> ·
091 <a href="./articles/nar2008_bibtex.txt">BibTeX</a> ]
092 </fieldset>
093
094 The previous DBD release (1.2) can be found in the <a href="/archive/DBD1.2/index.cgi?Home">archive</a>.
095 """ %({"url" : globals.HomeURLBase})
096
097
098 cellend()
099
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Traceback (most recent call last):
File "/net/isilonP/public/rw/research/teichmann/apache/test/DBD/web.py", line 148, in gen_cell
exec _code in _globals_d, _locals_d
File "<string>", line 23, in <module>
File "/net/isilonP/public/rw/research/teichmann/apache/test/DBD/dbd.py", line 528, in get_individual_genome_count
c = get_db_cursor()
File "/net/isilonP/public/rw/research/teichmann/apache/test/DBD/dbd.py", line 68, in get_db_cursor
db = MySQLdb.connect(host="mysql-teichmann-web.ebi.ac.uk", port=4412, user="admin", passwd="z2Kd6OvN", db="DBD2")
File "/usr/lib64/python2.6/site-packages/MySQLdb/__init__.py", line 81, in Connect
return Connection(*args, **kwargs)
File "/usr/lib64/python2.6/site-packages/MySQLdb/connections.py", line 187, in __init__
super(Connection, self).__init__(*args, **kwargs2)
OperationalError: (2005, "Unknown MySQL server host 'mysql-teichmann-web.ebi.ac.uk' (1)")
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