Pecinka lab:Resources

From OpenWetWare

Pecinka group2.jpg

Home      Research      People      Publications      Protocols      Resources      Seminars      Positions      Lab life     

General DNA Analysis and Database Tools

NCBI and NCBI BLAST. Multi-organismal National Center for Biotechnology database of sequences, alignment, blast and other tools.

EMBL-EBI. Multi-sequence alignment tool.

PHYTOZOME. Plant comparative genomics tool run by the DOE JGI.

PLANT GENOME DUPLICATION DATABASE. A good tool for finding synteny or paralogs.

CHROMATIN DATABASE. See an extensive list of genes associated with chromatin related processes.

REPBASE. Multi-species database of repetitive elements. Requires registration.

CyMATE and KISMETH. Bisulfite sequencing analysis tools.

Publicly Available Arabidopsis Software Tools

TAIR. The basic source of information (not only) for Arabidopsis. For an information on the world after TAIR see the International Arabidopsis Informatics Consortium

AtENSEMBL. Basic Arabidopsis genome browser. Handy for checking available mutants and their quick ordering thanks to the link with NASC collections.

SALK SIGnAL. Bunch of resources for Arabidopsis work, e.g. T-DNA orientation finder, 'SALK Epigenome' etc.

EXPRESSION DATA in eFP BROWSER. Even your grandma will understand gene expression with this tool.
GENEVESTIGATOR. Gene expression analysis center containing more datasets than eFP browser and also several other tools. Requires registration.

1001 GENOMES, SALK 1001 GENOMES BROWSER. Great source of data for natural variation analysis.

GWAPP. Web based GWAs application from the Nordborg lab.

'UCLA Epigenome', 'SALK Epigenome', 'CSHL Natural variation Epigenome'. Genome-wide distribution of many diagnostic chromatin marks in Arabidopsis at the websites run by the Jacobsen/Pellegrini's labs, the SALK institute and the Martienssen lab, respectively.

Plant DNA C-values database from MD Bennett and IJ Leitch.


R and RSTUDIO. Downloads, documentation, help etc. Some easy to understand help can be found also on Quick-R.



Current Biology

Current Opinion in Plant Biology

Genes & Development


Plant Cell

Plant Journal

Plant Physiology

PLoS Biology

PLoS Genetics

PLoS One

Proceedings of the National Academy of Sciences (PNAS)


Trends in Genetics

Trends in Plant Science