Interaction of Plant-Environment Lab

Plant Gene Set Enrichment / GO analysis

http://structuralbiology.cau.edu.cn/PlantGSEA/

 

GO analysis_AgriGO

http://systemsbiology.cau.edu.cn/agriGOv2/index.php

 

Heatmap

http://www1.heatmapper.ca/expression/

 

Design of qRT-PCR primers

http://atrtprimer.kaist.ac.kr/

 

Multiple protein sequences alignment

http://www.ebi.ac.uk/Tools/msa/muscle/

 

ePLANT

http://bar.utoronto.ca/eplant/

Tissue, specific expression similar to bar.

http://efp.ucr.edu/cgi-bin/relative.cgi (another cell type specific expression browser)

 

String - protein-protein interaction

http://string-db.org/

 

Mapman

http://mapman.gabipd.org/web/guest

 

 

qPCR primer design

http://www.quantprime.de/?page=home

 

 

Scripture

http://www.broadinstitute.org/software/scripture/

 

 

lncRNA genome brower

http://chualab.rockefeller.edu/cgi-bin/gb2/gbrowse/arabidopsis/

 

 

Plant small RNA target finder

http://plantgrn.noble.org/psRNATarget/

 

RNA secondary structure prediction

http://rna.tbi.univie.ac.at/cgi-bin/RNAfold.cgi

 

Dnase-Seq

http://www.plantregulome.org/

 

Brassica database

http://brassicadb.org/brad/index.php

 

Protein subcellular localization

http://www.csbio.sjtu.edu.cn/bioinf/Cell-PLoc-2/

 

Circadian clock

http://diurnal.mocklerlab.org/

 

Positive / negative selection

www.datamonkey.org

 

Arabidopsis bulk sequence download

http://www.arabidopsis.org/tools/bulk/sequences/index.jsp

 

CRISPR gRNA design

http://chopchop.cbu.uib.no/search.php

http://www.e-crisp.org/E-CRISP/index.html

 

Brassica rapa (Chiifu-401) genome database

http://brassicadb.org/brad/

 

Transmembrane domain prediction

http://www.ch.embnet.org/software/TMPRED_form.html

http://www.cbs.dtu.dk/services/TMHMM/

 

AlBERTO AraBidopsis Embryonic and Root Transcriptome brOwser

http://albertodb.org/#nav-start

 

Melting Curve Prediction

https://www.dna.utah.edu/umelt/um.php

 

Phylogenic tree generator

http://www.trex.uqam.ca/index.php?action=newick&project=trex

 

Heatmap

http://www.heatmapper.ca/expression/

https://software.broadinstitute.org/morpheus

 

Plot

https://huygens.science.uva.nl/PlotsOfData/