Pecinka lab:Resources: Difference between revisions
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[http://www.girinst.org/repbase/ REPBASE]. Multi-species database of repetitive elements. Requires registration. | [http://www.girinst.org/repbase/ REPBASE]. Multi-species database of repetitive elements. Requires registration. | ||
[http://www.cymate.org/ CyMATE] and [http://katahdin.mssm.edu/kismeth/revpage.pl KISMETH]. Bisulfite sequencing analysis tools. | |||
==Publicly Available Arabidopsis Software Tools== | ==Publicly Available Arabidopsis Software Tools== | ||
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[http://gwas.gmi.oeaw.ac.at/index.html#!homePage GWAPP]. Web based GWAs application from the Nordborg lab. | [http://gwas.gmi.oeaw.ac.at/index.html#!homePage GWAPP]. Web based GWAs application from the Nordborg lab. | ||
[http://epigenomics.mcdb.ucla.edu/DNAmeth/ 'UCLA Epigenome'], [http://neomorph.salk.edu/epigenome/epigenome.html 'SALK Epigenome'], [http://chromatin.cshl.edu/cgi-bin/gbrowse/epivariation/ '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. | [http://epigenomics.mcdb.ucla.edu/DNAmeth/ 'UCLA Epigenome'], [http://neomorph.salk.edu/epigenome/epigenome.html 'SALK Epigenome'], [http://chromatin.cshl.edu/cgi-bin/gbrowse/epivariation/ '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. | ||
[http://data.kew.org/cvalues/ Plant DNA C-values] database from MD Bennett and IJ Leitch. | |||
==R== | ==R== | ||
Latest revision as of 03:35, 1 November 2012
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Centre of Plant Structural and Functional Genomics |
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
R and RSTUDIO. Downloads, documentation, help etc. Some easy to understand help can be found also on Quick-R.
Journals
Current Opinion in Plant Biology
