Difference between revisions of "Maeda Lab:Protocols"
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<center> | <center> | ||
| − | [[Main_Page| <font face=" | + | [[Main_Page| <font face="Georgia" style="color:#ffffff" size=4> '''Home''' </font>]] |
| − | [[Maeda Lab:Research | <font face=" | + | [[Maeda Lab:Research | <font face="Georgia" style="color:#ffffff" size=4> '''Research''' </font>]] |
| − | [[Maeda Lab:Lab | + | [[Maeda Lab:Outreach | <font face="Georgia" style="color:#ffffff" size=4> '''Outreach''' </font>]] |
| − | [[Maeda Lab: | + | [[Maeda Lab:Diversity | <font face="Georgia" style="color:#ffffff" size=4> '''Diversity''' </font>]] |
| − | [[Maeda Lab: | + | [[Maeda Lab:Lab Members | <font face="Georgia" style="color:#ffffff" size=4> '''Team''' </font>]] |
| − | [[Maeda Lab: | + | [[Maeda Lab:Publications | <font face="Georgia" style="color:#ffffff" size=4> '''Pubs''' </font>]] |
| + | [[Maeda Lab:Protocols | <font face="Georgia" style="color:#ffffff" size=5> '''Protocols''' </font>]] | ||
</center> | </center> | ||
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| + | ==<h3><font>Resources</font></h3>== | ||
| + | '''<Clones>''' | ||
| + | *[https://nfluxmap.github.io/resources/ '''Aminotransferase genes from ''E. coli, Arabidopsis, and sorghum'''''] were synthesized through the '''DOE JGI Community Science Program (CSP award 503757)''' and are available to the scientific community. | ||
| + | **If you are interested in obtaining some of these clones, please look at our [https://nfluxmap.github.io/ '''DOE project website'''] and contact Hiroshi Maeda, University of Wisconsin-Madison at maeda2@wisc.edu. | ||
| + | |||
| + | '''<Codes>''' | ||
| + | *Codes that we used in our studies are made available at [https://github.com/HiroshiLab Github for '''Hiroshi Maeda Lab''']. | ||
| + | **[https://github.com/HiroshiLab/michaelis-menten R script for evaluating Michaelis-Menten kinetic parameters] | ||
| + | **[https://github.com/HiroshiLab/significance-in-plots ANOVA and Tukey-HSD post-hoc tests] | ||
| + | **[https://github.com/HiroshiLab/Building-gene-trees Building gene trees] | ||
| + | **[https://github.com/HiroshiLab/Evolutionary-rate Evolutionary-rate analysis] | ||
| + | **[https://github.com/HiroshiLab/RNA-seq_data_processing RNAseq data processing] | ||
| + | **[https://github.com/HiroshiLab/GO-term-enrichment GO-term-enrichment] | ||
| + | |||
==<h3><font>Protocols</font></h3>== | ==<h3><font>Protocols</font></h3>== | ||
'''<Molecular Biology>''' | '''<Molecular Biology>''' | ||
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*Sequence analysis | *Sequence analysis | ||
| + | **[https://www.bioinfodata.org/Blast4OneKP/home 1000 Plants (1KP) BLAST] | ||
**[http://blast.ncbi.nlm.nih.gov/Blast.cgi NCBI Blast] | **[http://blast.ncbi.nlm.nih.gov/Blast.cgi NCBI Blast] | ||
**[http://ffas.burnham.org/ffas-cgi/cgi/document.pl Fold & Function Assignment System (FFAS)] | **[http://ffas.burnham.org/ffas-cgi/cgi/document.pl Fold & Function Assignment System (FFAS)] | ||
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**[http://www.ch.embnet.org/software/BOX_form.html BoxShade] | **[http://www.ch.embnet.org/software/BOX_form.html BoxShade] | ||
***Select "RTF_new" and "ALN" | ***Select "RTF_new" and "ALN" | ||
| + | **[http://prodata.swmed.edu/promals3d/promals3d.php PROMALS3D], structure-guided phylogenetic analysis | ||
| + | ***Choose fasta output format in PROMALS3D | ||
| + | ***Select all the text and save as a .txt file. | ||
| + | ***In [http://www.megasoftware.net MEGA] go to File and select "convert file format to mega file". | ||
| + | ***Select the .txt file and specify fasta format. A new window will pop up to save as a new mega file. | ||
| + | ***Close out of this | ||
| + | ***Go to File, "open file/session", open the newly created mega file. | ||
| + | ***Run phylogenetic analyses. | ||
**[http://www.bioinformatics.org/sms/rev_comp.html Reverse Complement] | **[http://www.bioinformatics.org/sms/rev_comp.html Reverse Complement] | ||
**[http://searchlauncher.bcm.tmc.edu/seq-util/Options/readseq.html Convert Sequence Format] | **[http://searchlauncher.bcm.tmc.edu/seq-util/Options/readseq.html Convert Sequence Format] | ||
**[http://web.expasy.org/translate/ Translate] | **[http://web.expasy.org/translate/ Translate] | ||
**Protein Targeting Prediction ([http://www.cbs.dtu.dk/services/ChloroP/ ChloroP], [http://urgi.versailles.inra.fr/predotar/predotar.html Predotar],[http://www.cbs.dtu.dk/services/TargetP/ TargetP], [http://wolfpsort.org/ PSORT]) | **Protein Targeting Prediction ([http://www.cbs.dtu.dk/services/ChloroP/ ChloroP], [http://urgi.versailles.inra.fr/predotar/predotar.html Predotar],[http://www.cbs.dtu.dk/services/TargetP/ TargetP], [http://wolfpsort.org/ PSORT]) | ||
| + | **[http://suba.plantenergy.uwa.edu.au/ '''SUBA3'''] (The SUBcellular localisation database for Arabidopsis proteins) | ||
| + | **[http://phylomedb.org/ '''PhylomeDB'''] (catalogs of gene phylogenies (phylomes) | ||
| + | **[http://biocyc.org/ '''Bio.Cyc'''] collection of 7667 Pathway/Genome Databases (PGDBs), plus software tools | ||
| + | **[http://aranet.mpimp-golm.mpg.de/index.html '''PlaNet'''] visualization and analysis of plant co-function networks | ||
| + | |||
'''<Biochemistry>''' | '''<Biochemistry>''' | ||
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==<h3><font>Useful links</font></h3>== | ==<h3><font>Useful links</font></h3>== | ||
*Research | *Research | ||
| + | **[http://kanaya.naist.jp/knapsack_jsp/top.html KNApSAcK metabolite-species search] | ||
**[http://biologylabs.utah.edu/jorgensen/wayned/ape/ ApE plasmid Editor] | **[http://biologylabs.utah.edu/jorgensen/wayned/ape/ ApE plasmid Editor] | ||
**[http://www.biosci.ohio-state.edu/pcmb/Facilities/abrc/handling.htm Arabidopsis growth ARBC] | **[http://www.biosci.ohio-state.edu/pcmb/Facilities/abrc/handling.htm Arabidopsis growth ARBC] | ||
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**[http://chapplewiki.wikispot.org/Protocols Clint Chapple Lab at Purdue University] | **[http://chapplewiki.wikispot.org/Protocols Clint Chapple Lab at Purdue University] | ||
**[http://www.youtube.com/watch?v=ATh7MljikaA Plasmid Isolation - Mini Prep video] | **[http://www.youtube.com/watch?v=ATh7MljikaA Plasmid Isolation - Mini Prep video] | ||
| + | **[http://medicago-mutant.noble.org/mutant/index.php Noble Foundation Medicago insertional mutant collection] | ||
*Others | *Others | ||
**[http://www.ehs.wisc.edu/chem-chemicaldisposalsurplus-chemicalwastesurpluspickuprequestform.htm Waste Pickup Request] | **[http://www.ehs.wisc.edu/chem-chemicaldisposalsurplus-chemicalwastesurpluspickuprequestform.htm Waste Pickup Request] | ||
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* [http://www.mediawiki.org/wiki/Manual:FAQ MediaWiki FAQ] | * [http://www.mediawiki.org/wiki/Manual:FAQ MediaWiki FAQ] | ||
* [https://lists.wikimedia.org/mailman/listinfo/mediawiki-announce MediaWiki release mailing list] | * [https://lists.wikimedia.org/mailman/listinfo/mediawiki-announce MediaWiki release mailing list] | ||
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