M.Sc. Bioinfo + 5 years industry exp. - - - Looking for a position in biosciences. I'm gifted at the command line or computer terminal, but I perform best on my feet, standups, cleaning, guitar with samples in the centrifuge, more in the water bath, data being processed on the computer while I sleep, and other assays to plan. Currently writing a DNA sequence graph algorithm and manuscript (for bioRxiv). I play math rock on my guitar, I have some open-source software on GitHub, I pay my bills in the DE-NJ-PA tri-state area near Delco, and I'm launching a DE-based LLC for Univ. of Delaware and local NGS sequencing projects.
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I want to discuss linear runtimes and what that means in alignment-free methods for bioinformatics and sequence alignments and quasi alignments. First, it is the splitting of the sequences, as they are read, into, let’s say, ‘a’ De Bruijn graph. This graph consists of the k-mers, their neighborhoods, and of course the walks or paths through the graph that constitute optimal criteria and local maxima of course for traversal and contig/walk/path maximization. Typically, a search through the De Bruijn structure may be Breadth-First to find optimal depths for traversal of the path through the De Bruijn structure, optimizing for creating some sequence. This leads to read collapse along the sequence unidirectionally (bidirectionally in a unidimensional space) along the sequence space.
