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I performed several BLAST searches and identified several genes of interest in a Whole Genome Shotgun (wgs) project. I know that gene X is located on scaffold 1234, from nucleotide 1 - 2250, while gene Y is located on scaffold 2571, from nucleotide 3380 - 5790.

Given this information is it possible to determine if these genes are close to each other in the genome?

Many thanks for your help,

  • Leah
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  • $\begingroup$ great question.. i guess if you cannot assemble the contigs, chances are you are unlikely to get it from the current dataset.. which organism is this? $\endgroup$
    – StupidWolf
    Apr 3, 2020 at 9:49
  • $\begingroup$ Thanks @StupidWolf! It is a wgs from an amoebozoan protist. $\endgroup$
    – Leah
    Apr 4, 2020 at 18:57
  • $\begingroup$ @michael, I would very much appreciate your thoughts on this question! $\endgroup$
    – Leah
    Apr 4, 2020 at 19:03

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