Chan:Bioinformatics Sites

From OpenWetWare

(Difference between revisions)
Jump to: navigation, search
Current revision (18:18, 28 October 2011) (view source)
m
 
(14 intermediate revisions not shown.)
Line 2: Line 2:
<br>
<br>
<center>
<center>
-
<font face="Helvetica" size=6 color=#556B2F>
+
<font face="Helvetica" size=6 color=#339900>
'''Chan Lab'''<br>
'''Chan Lab'''<br>
</font>
</font>
<br>
<br>
-
[http://www-plb.ucdavis.edu/index.html Department of Plant Biology] at [http://www.ucdavis.edu/ UC Davis]
+
[http://www-plb.ucdavis.edu/ Department of Plant Biology], [http://www.ucdavis.edu/ UC Davis] and [http://www.hhmi.org HHMI]
</center>
</center>
----
----
Line 13: Line 13:
{| cellspacing="3"  
{| cellspacing="3"  
|- valign="top"
|- valign="top"
-
|width=200px rowspan=2 class="MainPageBG" style="border: 0px solid #cc3300; color: #9ACD32; background-color: #ffffff"|
+
|width=200px rowspan=2 class="MainPageBG" style="border: 0px solid #cc3300; color: #339900; background-color: #ffffff"|
<div style="padding: .4em .9em .9em">
<div style="padding: .4em .9em .9em">
[[Chan|Home]]
[[Chan|Home]]
Line 26: Line 26:
----
----
[[Chan:Bioinformatics Sites|Bioinformatics]]
[[Chan:Bioinformatics Sites|Bioinformatics]]
-
----
 
-
[[Chan:Teaching|Teaching]]
 
----
----
[[Chan:Contact|Contact]]
[[Chan:Contact|Contact]]
Line 49: Line 47:
[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>
 +
----
 +
<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>
----
----
<b>Bioinformatics:</b><br>
<b>Bioinformatics:</b><br>
Line 59: Line 62:
[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://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://inparanoid.sbc.su.se/cgi-bin/index.cgi Inparanoid homolog search]<br>
 +
[http://meme.nbcr.net/meme/intro.html MEME motif finder]<br>
----
----
<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>
----
----
<b>Literature:</b><br>
<b>Literature:</b><br>

Current revision


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

Personal tools