Computational protocol: Use of MSAP Markers to Analyse the Effects of Salt Stress on DNA Methylation in Rapeseed (Brassica napus var. oleifera)

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Protocol publication

[…] The sequences were aligned along two Brassica genomes, as well as the Arabidopsis genome, using different BLAST based approaches []. In particular, a BLASTn analysis was used to compare the 24 sequenced bands to the two assembled Brassica genomes B . rapa (Chiifu-401, version 1.1) and B. oleracea (version 2011-08-02-BGI), and also for a comparison with the A. thaliana (version TAIR10 []) genome. A tBLASTx analysis was also performed with the B . rapa and A. thaliana genome sequences in order to identify similarities in protein-coding regions. This type of BLAST translates both the query and the subject sequence in all possible reading frames. In order to confirm the presence of the methylated fragments along the Brassicaceae genomes, we also performed a BLASTn alignment versus The Sequence Read Archive (SRA) [], where the raw sequence data from B . rapa and its subspecies B . rapa subsp. Pekinensis (Chinese cabbage) are stored (http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi). Finally for each sequence that showed an alignment to the B . rapa chromosome, the presence of genes both in the alignment region and in the flaking ones were checked, using the Brassica database annotation [].In order to enrich the functional description we compiled a Gene Ontology annotation, using the BLAST2GO at the AmiGO web site [] and setting a cut-off e-value of 0.001. […]

Pipeline specifications

Software tools BLASTN, TBLASTX, Blast2GO, AmiGO
Databases TAIR BRAD
Application Nucleotide sequence alignment
Organisms Brassica napus
Chemicals Cytosine, Trehalose