I am new to bioinformatics and just for the sake of this question, suppose that I am looking for the full genome sequence of [*Escherichia coli*][1] and [*Saccharomyces cerevisiae*][2] in FASTA format. I thought that these would be fairly easy to find online.

For Escherichia coli I was only able to find some links to the ncbi website but I could not find anywhere in the website a link to download the genome in FASTA format. For Saccharomyces cerevisiae, I found [this FTP site][3] linked by ensembl with the sequence for each chromosome. I suppose that I could concatenate all the files in order to obtain the full genome in one file but isn't there already one file with the entire sequence? I saw the top level files but those only appear for masked and soft masked DNA, I think it would be doable to work with those if modern sequencers masked the DNA automatically, do they?

So, in summary, how do experienced people find full reference genomes for those two organisms and possibly other common species? I have only been using Google and the only page that appears to provide FASTA files for some species is Ensembl.

 [1]: http://en.wikipedia.org/wiki/Escherichia_coli
 [2]: http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae
 [3]: ftp://ftp.ensembl.org/pub/current_fasta/saccharomyces_cerevisiae/dna/
<p>First place to check is Ensembl. They have separate pages for <a href="http://metazoa.ensembl.org/">metazoa</a>, <a href="http://fungi.ensembl.org/">fungi</a>, etc. as well as the normal <a href="http://www.ensembl.org/info/about/species.html">vertebrate page</a> (which also contains S. cerevisiae). Each of the sites have a <a href="http://www.ensembl.org/info/data/ftp/index.html">download page</a> (click on &quot;Downloads&quot; at the top and then &quot;Download data via FTP&quot; on the right), where you can easily find fasta/GTF/etc. files.</p>

<p>BTW, a soft-masked genome is the genome. Soft-masking just means that predicted repeat regions are lower-case.</p>

<p>A second BTW is that you&#39;ll usually want the &quot;toplevel&quot; file.</p>
