I read that the genome for Malus Domestica was mapped, but I can't find a sequence anywhere.
If this is a stupid question, I would appreciate if you would please tell me where I am wrong in this!
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$\begingroup$ Googled "malus domestica genome sequence". First result was this paper, which includes this genome bank entry (which is also the second search result) $\endgroup$– LuigiCommented Jul 27, 2015 at 17:57
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$\begingroup$ @Luigi Thanks, but I don't know how to make sense of the genome bank entry $\endgroup$– Luke DinklerCommented Jul 27, 2015 at 20:15
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$\begingroup$ If all you want is to download the sequence of all the chromosomes, look at the haplotype assembly. Download the first file (psuedomolecules) and unzip it. Then you'll have the sequence of each chromosome in FASTA format. $\endgroup$– LuigiCommented Jul 27, 2015 at 21:10
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2 Answers
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https://www.rosaceae.org/species/malus/malus_x_domestica/genome_v1.0
You can see the data in the URL above. The details are described in this article.
As others said, NCBI seems useful. Go to this site. Chose chromosome you want to see and click genebank or refsequence corresponding to the chromosome in the table (Assembly Unit: Primary Assembly). You can see overview of the sequence. Find FASTA in the page showing the overview and click FASTA. Then the sequence data will be downloaded.
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$\begingroup$ Thank you, I had a look at the above link, but I'm still not seeing the DNA nucleotide sequence. $\endgroup$ Commented Jul 27, 2015 at 20:14
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$\begingroup$ The sequence data is shown like rosaceae.org/gb/gbrowse/malus_x_domestica You might be able to extract sequences from this. But I have not used this particular site. At least, you can see the conting sequences indicated in red by clicking the red areas like rosaceae.org/gb/malus_details?id=1311210 $\endgroup$– 243Commented Jul 27, 2015 at 20:29
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$\begingroup$ Thanks for your help. I used the DNA database at ncbi.nlm.nih.gov to find the answer $\endgroup$ Commented Jul 27, 2015 at 20:34
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Here is the apple genome on NCBI.
answered Jul 27, 2015 at 20:39
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$\begingroup$ How many lines of nucleotide sequences are there? $\endgroup$ Commented Jul 27, 2015 at 20:55
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$\begingroup$ Are all sequence lines necessary? $\endgroup$ Commented Jul 27, 2015 at 21:00