Chan:Bioinformatics Sites: Difference between revisions

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[[Chan|Chan Lab Homepage]]<br>
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'''Chan Lab'''<br>
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<br>
[http://www-plb.ucdavis.edu/ Department of Plant Biology], [http://www.ucdavis.edu/ UC Davis] and [http://www.hhmi.org HHMI]
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[[Chan|Home]]
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[[Chan:Research|Research]]
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[[Chan:Publications|Publications]]
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[[Chan:People|People]]
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[[Chan:Links|Links]]
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[[Chan:Bioinformatics Sites|Bioinformatics]]
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[[Chan:Contact|Contact]]
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<b>Arabidopsis tools:</b><br>
<b>Arabidopsis tools:</b><br>
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[http://atensembl.arabidopsis.info/index.html AtEnsembl]<br>
[http://atensembl.arabidopsis.info/index.html AtEnsembl]<br>
[http://www.weigelworld.org/resources WeigelWorld Resources incl. AtGenExpress]<br>
[http://www.weigelworld.org/resources WeigelWorld Resources incl. AtGenExpress]<br>
[http://mocklerlab.cgrb.oregonstate.edu/ Todd Mockler expression tools]<br>
[http://epigenomics.mcdb.ucla.edu/DNAmeth/ Jacobsen/Ecker Arabidopsis Methylome Database]<br>
[http://epigenomics.mcdb.ucla.edu/DNAmeth/ Jacobsen/Ecker Arabidopsis Methylome Database]<br>
[http://asrp.cgrb.oregonstate.edu/ Carrington Lab siRNA Database]<br>
[http://asrp.cgrb.oregonstate.edu/ Carrington Lab siRNA Database]<br>
[http://mpss.udel.edu/at/ MPSS Small RNAs and Transcripts]<br>
[http://mpss.udel.edu/at/ MPSS Small RNAs and Transcripts]<br>
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<b>Yeast Genome Databases:</b><br>
[http://www.genedb.org/genedb/pombe/ ''S.pombe'' genome database]<br>
[http://www.yeastgenome.org/ ''S.cerevisiae'' genome database]<br>
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<b>Bioinformatics:</b><br>
<b>Bioinformatics:</b><br>
[http://www.ncbi.nlm.nih.gov/ NCBI homepage]<br>
[http://www.ncbi.nlm.nih.gov/blast/ BLAST at NCBI]<br>
[http://www.ncbi.nlm.nih.gov/blast/ BLAST at NCBI]<br>
[http://www.ncbi.nlm.nih.gov/BLAST/Genome/PlantBlast.shtml BLAST Plant Genomes]<br>
[http://www.ncbi.nlm.nih.gov/BLAST/Genome/PlantBlast.shtml BLAST Plant Genomes]<br>
[http://smart.embl-heidelberg.de/ SMART Protein Domains]<br>
[http://smart.embl-heidelberg.de/ SMART Protein Domains]<br>
[http://www.ebi.ac.uk/clustalw/ ClustalW at EBI]<br>
[http://www.ebi.ac.uk/clustalw/ ClustalW at EBI]<br>
[http://bibiserv.techfak.uni-bielefeld.de/dialign/submission.html Dialign multiple sequence alignment]<br>
[http://www.sanger.ac.uk/PostGenomics/S_pombe/YOGY/ YOGY homolog search]<br>
[http://inparanoid.sbc.su.se/cgi-bin/index.cgi Inparanoid homolog search]<br>
[http://meme.nbcr.net/meme/intro.html MEME motif finder]<br>
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<b>Experimental:</b><br>
<b>Experimental:</b><br>
[http://frodo.wi.mit.edu/cgi-bin/primer3/primer3_www.cgi Primer3]<br>
[http://www3.interscience.wiley.com/browse/?type=CURRENT_PROTOCOL Current Protocols]<br>
[http://frodo.wi.mit.edu/primer3/ Primer3]<br>
[http://www.basic.northwestern.edu/biotools/oligocalc.html Oligo Calculator]<br>
[http://www.basic.northwestern.edu/biotools/oligocalc.html Oligo Calculator]<br>
[http://rebase.neb.com/rebase/rebase.html REBase at NEB]<br>
[http://rebase.neb.com/rebase/rebase.html REBase at NEB]<br>
[http://helix.wustl.edu/dcaps/dcaps.html dCAPs Finder]<br>
[http://helix.wustl.edu/dcaps/dcaps.html dCAPs Finder]<br>
 
[http://www.fourmilab.ch/rpkp/experiments/analysis/chiCalc.html Chi-square calculator]<br>
[http://www.fourmilab.ch/rpkp/experiments/analysis/chiCalc.html Chi-square calculator]
[http://www.proweb.org/coddle/ CODDLE for TILLING]<br>
[http://www-rcf.usc.edu/~forsburg/#info Forsburg lab S.pombe methods]<br>
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<b>Literature:</b><br>
<b>Literature:</b><br>
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[http://scholar.google.com/ Google Scholar]<br>
[http://scholar.google.com/ Google Scholar]<br>
<br>
<br>
[[Chan|Chan Lab Homepage]]<br>
 
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Latest revision as of 16:18, 28 October 2011


Chan Lab
Department of Plant Biology, UC Davis and HHMI


Arabidopsis tools:
TAIR BLAST search
TIGR Arabidopsis BLAST Search
Salk Institute Genome Analysis Laboratory (SIGnaL) T-DNA Express
Primer design for T-DNAs
Dirk Inze GATEWAY vectors

Arabidopsis genome databases:
TAIR (The Arabidopsis Information Resource)
TAIR Seqviewer
AtEnsembl
WeigelWorld Resources incl. AtGenExpress
Todd Mockler expression tools
Jacobsen/Ecker Arabidopsis Methylome Database
Carrington Lab siRNA Database
MPSS Small RNAs and Transcripts

Yeast Genome Databases:
S.pombe genome database
S.cerevisiae genome database

Bioinformatics:
NCBI homepage
BLAST at NCBI
BLAST Plant Genomes
SMART Protein Domains
ClustalW at EBI
Dialign multiple sequence alignment
YOGY homolog search
Inparanoid homolog search
MEME motif finder

Experimental:
Current Protocols
Primer3
Oligo Calculator
REBase at NEB
dCAPs Finder
Chi-square calculator
CODDLE for TILLING
Forsburg lab S.pombe methods

Literature:
NCBI
ISI Knowledge
Google Scholar

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