looking for DNA Sequencing for high quality genome assemblying

Discussion in 'Plants: Science and Cultivation' started by MelMartin, Dec 18, 2015.

  1. MelMartin

    MelMartin New Member

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    Hi all,
    I am a student in Bioinformatics at TUDelft in the Netherlands. My current research focus on developping a new algorithm to assembly aneuploid organisms. Most mammals are diploid (they have two sets of each chromosomes) most bacteria have a single strain of their genome (haploid) many crops plants are polyploid (have a regular set of chromosomes:tetraploid, triploid, etc...) Aneuploid organisms have different number for each chromosomes. I originally started my research with yeast, then realized that I was actualy working for a beer company interested in improving their fermentation process. I would like to apply my method to genomes with more motivating applications. I was originally thinking about medicinal plants and started to search for open source dna sequence reads of Banisteriopsis caapi. In one thread someone mentioned its genome could exist in the World Gene Bank but couldn't find it and I am not even sure its ploidity would suit my algorithm. My question is: Do you know where the ploidity (number of chromosome sets) of a certain plant/fungi can be checked and; where could I find open source raw reads(dna sequencing) of these genomes? Many thanks
     
  2. vitog

    vitog Well-Known Member

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    Try Googling the plant/fungus of interest and "ploidy". For DNA sequencing, GenBank at GenBank Home is described as "an annotated collection of all publicly available DNA sequences".
     
  3. Daniel Mosquin

    Daniel Mosquin Renowned Contributor UBC Botanical Garden Forums Administrator Forums Moderator 10 Years

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  4. MelMartin

    MelMartin New Member

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    That is a wonderful resource... Thanks a lot Daniel!!
     

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