Pecinka Lab:Resources: Difference between revisions
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==General DNA Analysis and Database Tools== | ==General DNA Analysis and Database Tools== | ||
[http://www.ncbi.nlm.nih.gov/ NCBI] and [http://blast.ncbi.nlm.nih.gov/ NCBI BLAST]. Multi-organismal National Center for Biotechnology database of sequences, alignment, blast and other tools. | [http://www.ncbi.nlm.nih.gov/ NCBI] and [http://blast.ncbi.nlm.nih.gov/ NCBI BLAST]. Multi-organismal National Center for Biotechnology database of sequences, alignment, blast and other tools. | ||
[http://www.ebi.ac.uk/Tools/msa/clustalw2/ EMBL-EBI]. Multi-sequence alignment tool. | |||
[http://genome.jgi.doe.gov/programs/plants/index.jsf PHYTOZOME]. Plant comparative genomics tool run by the [http://www.jgi.doe.gov/ DOE JGI]. | [http://genome.jgi.doe.gov/programs/plants/index.jsf PHYTOZOME]. Plant comparative genomics tool run by the [http://www.jgi.doe.gov/ DOE JGI]. | ||
Revision as of 11:48, 23 June 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.
Publicly Available Arabidopsis Software Tools
TAIR. The basic source of information (not only) for Arabidopsis.
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'. Genome-wide distribution of many diagnostic chromatin marks in Arabidopsis at the websites run by the Jacobsen/Pellegrini's labs or the SALK institute, respectively.
R
R and RSTUDIO. Downloads, documentation, help etc. Some easy to understand help can be found also on Quick-R.
