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  • Apllications of Graph Theory in Next Generation Sequencing

    Hello everyone,

    I'm a math student interested in graph theory and its applications in biology. Sadly, biomathmeatics and bioinformatics in general are somewhat neglected at my university.

    During my next semester, I'll have 2-3 months to write a paper on a topic of my choosing and I've thought about doing something relaxted to Next Generation Sequencing.
    I'm currently doing an out-of-university-internship where I have to work with some Next Generation Assembly programs, so I've heard of De Bruijn Graphs and their role in assembly. However, I am not sure whether this topic by itself would be complex enough to devote my whole paper to it, so I'm currently looking for further ideas for a possible topic.
    Can anyone point me to other areas of Next Generation Sequencing / genetics / bioinformatics where graph theory is applied?

    Thank you for your answers
    Martin

  • #2
    Recently a nice review was suggested to learn about genome assembly using De Bruijn graphs. You may want to look at transcriptome assembly too. I would say that there is quite a lot to read and write on graphs for NGS.
    Graphs are used in many applications.. right away I would cite "splicing graph" for instance, but as Directed Acyclic Graphs can easily substitute Hidden Markov Models you may find them in problems like gene finding or multiple alignment.
    I would browse pubmed, like this for instance or like this.

    Now maybe others will contribute with better propositions..

    Anyway, thanks for your interest, good luck and enjoy!

    Comment


    • #3
      Sadly Graph Theory doesn't help very much in biology. Graph applications on the other hand are very valuable. If you know what I mean.

      Comment


      • #4
        There has been some use of graph theory in haplotyping. See:


        Comment

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