Assmann Lab presents
Orzya CLIMtools
Created by Ángel Ferrero-Serrano and Sally Assmann
Please cite: Ferrero-Serrano Á, Chakravorty D, Kirven KJ, Assmann SM. 2024
Oryza CLIMtools: A genome–environment association resource reveals adaptive roles for heterotrimeric G proteins in the regulation of rice agronomic traits,
Plant Communications, PMID: 38213027, https://doi.org/10.1016/j.xplc.2024.100813.
Arabidopsis CLIMtools
Created by Ángel Ferrero-Serrano and Sally Assmann
Please cite: Ferrero-Serrano Á, Assmann SM. 2019
Phenotypic and genome-wide association with the local environment of Arabidopsis.
Nature Ecology and Evolution PMID:30643246, doi: 10.1038/s41559-018-0754-5
CLIM Tools
Protocols
Some of the protocols we use are available from the links below.
-
Rice CRISPR protocol
-
Preparation of Epidermal Peels and Guard Cell Protoplasts
-
pDOE BiFC Vectors
-
Biolistic Transformation of Guard Cells
-
Gas Exchange
-
Plant Electrophysiology
Software
StructureFold2 is our signature bioinformatic tool to analyze in vivo RNA- structuromes using chemically probed RNA libraries. It is currently hosted on GitHub and frequently updated. Included on GitHub is an easy to follow manual.
StructureFold2 Dependencies
- cutadapt – read adapter and quality trimmer.
- Bowtie2 – Fast and sensitive read alignment.
- SAMtools – tools for working with the SAM/BAM format.
- RNAstructure package – folds RNA with constraints
- Vienna Package – folds RNA without constraints
We highly reccomend learning and using Python for most common bioinformatic tasks, as it is a versitile, easy to learn scripting language, with a fully developed host of resources.
We highly reccomend learning and using R for all statistical needs, as well as chart and graph generation. R has an almost endless variety of packages, custom-tailored for almost any sort of analysis.
Scientific Links
Arabidopsis Information Portal (Araport)
The Arabidopsis Information Resource (TAIR)
Nottingham Arabidopsis Stock Centre (uNASC)
The Salk Institute Genomic Analysis Laboratory
National Center for Biotechnology Information Site
Online Analytical Tool link pages
- Biological Information Resource (U. of Washington)
- ABIM Online Analysis Tools (Université Aix-Mairseille)
- MEME Motif Scan
Other
- AGRICOLA, USDA National Agricultural Library
- How to think like a computer scientist – Start learning Python here!