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I am currently working through the code example on the MATLAB website. It requires me to download the reference genome of Arabidopsis thaliana (thale cress) so I can use BowTie2 to align the Chip-Seq experiment data. I need it in a .fa file.

Since I am very very new to this, what is the database where I can use to download this reference genome? How do I search for something like this? Thanks

EDIT: spoke too soon. I think the NCBI website did it for me. Under the Representitive -> Reference genome section. Is this correct?

EDIT2: The answer was in the MATLAB page also. The bioinformatics toolbox provides a function:

% getgenbank('NC_003070','FileFormat','fasta','tofile','ach1.fasta');
% getgenbank('NC_003071','FileFormat','fasta','tofile','ach2.fasta');
% getgenbank('NC_003074','FileFormat','fasta','tofile','ach3.fasta');
% getgenbank('NC_003075','FileFormat','fasta','tofile','ach4.fasta');
% getgenbank('NC_003076','FileFormat','fasta','tofile','ach5.fasta');
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Since you are using Bowtie, you want the indexed genome, see if that's not available here, instead of downloading the fasta and indexing it yourself.

http://support.illumina.com/sequencing/sequencing_software/igenome.ilmn

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