DBD: Transcription factor prediction database

Release 2.0
www.transcriptionfactor.org
Sequence ID search:
Introduction

DBD is a database of predicted transcription factors in completely sequenced genomes.
The predicted transcription factors all contain assignments to sequence specific DNA-binding domain families. The predictions are based on domain assignments from the SUPERFAMILY and Pfam hidden Markov model libraries. Benchmarks of our transcription factor predictions show they are accurate and have wide coverage on a genomic scale.
The DBD consists of predicted transcription factor repertoires for
An error occured in context "Home" cell "0.01"
in the section containing the code:
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> ] &nbsp;
052 <b>Full text</b> [ <a href="http://nar.oxfordjournals.org/content/38/21/7364.long">HTML</a> &#183;
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> ] &nbsp;
068 <b>Full text</b> [ <a href="http://www.sciencedirect.com/science/article/pii/S0168952510001277">HTML</a> &#183;
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> ] &nbsp; 
085 <b>Full text</b> [ <a href="http://nar.oxfordjournals.org/cgi/content/full/36/suppl_1/D88">HTML</a> &#183; 
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> &#183;
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 
Traceback (most recent call last):
  File "/net/isilonP/public/rw/research/teichmann/apache/live/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/live/DBD/dbd.py", line 528, in get_individual_genome_count
    c = get_db_cursor()
  File "/net/isilonP/public/rw/research/teichmann/apache/live/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: (2003, "Can't connect to MySQL server on 'mysql-teichmann-web.ebi.ac.uk' (111)")

Recent news
Recent updates to DBD
9th Nov 2011 Pedobacter Heparinus genome is added ... Further details
30th Aug 2008 New fungal genomes ... Further details
20th Aug 2008 Integrated transcription factor predictions for the Dictyostelium purpureum genome ... Further details
18th Aug 2008 Added domain assignments for over 50 bacterial genomes from the NCBI ... Further details
11th Aug 2008 Reclassified 8 domains ... Further details
8th Aug 2008 Transcription factor predictions for new green algae Ostreococcus RCC809.
Further details on recent updates to DBD can be found in the News archive.