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So I need to learn how to find the sequence of a gene, polyphenoloxidase. Please do not do this for me. Tell me how to approach the problem.

I have found : https://www.ncbi.nlm.nih.gov/gene and searched for polyphenoloxidase and get a list of results.

Here is one PPO page: https://www.ncbi.nlm.nih.gov/gene/107923401 There is a FASTA sequence there under " NC_030099.1 Reference ASM98774v1 Primary Assembly" but I am not sure if PPO gene is there.

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  • $\begingroup$ You need a gene sequence. What're you trying to accomplish? The list you get from the NCBI search notes PPO in different isoforms/types from different species. Perhaps you should first lock down your target organism and gene isoform. And so I click the top result, LOC107923401 (aka PPO-3; PPO-6; PPO-8) from Cotton. Scroll down to Genomic regions, transcripts, and products and click on the FASTA link. There is the raw sequence. Your FASTA and FASTQ files will be the result of NGS on your organism's genome. $\endgroup$
    – CKM
    Jun 11, 2018 at 18:49
  • $\begingroup$ @CKM advocado is my target organism. $\endgroup$
    – Dale
    Jun 11, 2018 at 18:52
  • $\begingroup$ If you want to blast that sequence, remove the subquery range it provides for you beside the sequence box. $\endgroup$
    – CKM
    Jun 11, 2018 at 18:52
  • $\begingroup$ @CKM Tried doing a Blast search for a PPO gene: ncbi.nlm.nih.gov/blast/… However there are no matches, which may be because it is a different species with a slightly different sequence? The genome I am searching is known to contain PPO. $\endgroup$
    – Dale
    Jun 11, 2018 at 18:54
  • $\begingroup$ It doesn't appear that anyone has sequenced it. See here. $\endgroup$
    – CKM
    Jun 11, 2018 at 19:05

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You can find the sequence in the gene database, but it is perhaps easier to search the nucleotide database if you are only looking for the sequence of nucleotides.

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  • $\begingroup$ I used the sequence you helped me find to do a Blast search of a genome here: blast.ncbi.nlm.nih.gov/… However there are no matches, which is may be because it is a different species with a slightly different sequence? The genome I am searching is known to contain PPO as advocados do brown. $\endgroup$
    – Dale
    Jun 11, 2018 at 18:39
  • $\begingroup$ @Dale It doesn't appear as though there is a whole genome sequence for avocado, yet. $\endgroup$
    – canadianer
    Jun 11, 2018 at 18:44
  • $\begingroup$ What about: ncbi.nlm.nih.gov/genome/?term=avocado $\endgroup$
    – Dale
    Jun 11, 2018 at 18:45
  • $\begingroup$ The existence of that page doesn't mean that the entire sequence is in the database. $\endgroup$
    – canadianer
    Jun 11, 2018 at 18:56
  • $\begingroup$ @Dale There are a large number of ESTs for avocado and blasting against those (tblastn) with the tomato PPO protein sequence gave some hits. $\endgroup$
    – canadianer
    Jun 11, 2018 at 18:57

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