Below is a quick summary of the work I’ve been doing in bioinformatics for my undegraduate independent research project.
My research is focused on bioinformatics – the use of computational methods to understand biological systems. In particular, I have been exploring ways to estimate the abundance of DNA segments (genes or genomes) within biological samples using high-throughput sequencing data. One application of this information is the study of the effects of the abundance of a certain bacteria on health or disease. Current methods for estimating abundances are either slow or not generally applicable and my work has been focused on changing this process through the use of k-mer counts (k-mers are substrings of DNA of length k).
K-mer analysis begins by counting the frequency of distinct k-mers in a sample of DNA and comparing these counts with k-mers found in a set of DNA fragments (contigs) of interest. While there are tools which use k-mer counts to estimate the abundance of genes in a particular sample, I have shown that they break down in metagenomic contexts – samples collected from the environment containing multiple organisms. Metagenomic samples contain many highly related organisms which leads to the presence of spurious counts when looking at a contig because of sequences originating from the related organisms (non-unique k-mers). In an attempt to recover a clean signal, I tried multiple methods to fit the distribution of observed counts to a statistical model as well as a variety of signal processing techniques. However, after months of negative results, my attention shifted to a novel application of k-mers: haplotype separation.
For diploid (two chromosomes) organisms, a sequenced genome is a mixture of two chromosomes (one from the mother and the other from the father). In order to label the haplotype profiles of a mother terrapin’s genome, we applied a k-mer analysis based on 16 of its progeny. I wrote software to collect k-mer counts from the 16 progeny and join them to create a k-mer presence/absence table. Doing so with over 3 billion distinct k-mers involved massaging hash tables for an efficient join as well as determining criteria for retaining an informative subset of k-mers. In a collaboration with students from the University of Tubingen, my software for labeling a sequence of DNA based on its consensus haplotype profile was used to annotate over 60% of the terrapin genome. By examining many samples, progeny in this case, k-mers give rise to a clearer picture than any single sample could provide. With this insight, I refocused my original k-mer analysis.
While abundance estimation using k-mer counts is still an open problem, one application of these estimates from multiple samples is to separate or cluster contigs based on the genome they originate from. This approach has been used with read-mapping data for de novo metagenomic assemblies. Read mapping is slow and involves an arbitrary choice of the “best” mapped location. I am currently investigating the effects of replacing read-mapping data with k-mer counts. The latter are much faster to compute and lead to a large efficiency gain when examining hundreds of samples. Barring success with the existing clustering algorithms, such as Gaussian mixture models and canopy, I will need to investigate the performance of a new clustering approach which is more closely aligned with the characteristics of k-mer counts. For example, even if the k-mer counts do not fit a clean statistical model, two contigs which originate from the same genome should have a low variance in the ratio of their counts. This metric lends itself well to graph clustering with canopy pre-processing in order to avoid computing distance metrics for all pairs.
Pending the success of this new approach, I will be able to explore the effect of k-mer size as well as selecting a subset of informative k-mers, much like in the haplotype project. K-mer size selection is not rigorously studied, but is very important from an engineering perspective. For example, at k = 15, a 4 byte counter can be used for each k-mer in a contiguous array with direct addressing (not storing keys) and still fit in a desktop’s memory; at k = 20, a sophisticated hash table must be used to fit the counts in a server’s memory. Research on the effect of k-mer size will enable further progress on previous work I put on hold – compactly storing k-mer counts for multiple samples and an exploration of whether approximate counts can be used (which can be computed more efficiently). The impact of positive findings in my research would lead to a space reduction of two orders of magnitude as compared to approaches that rely on the raw reads.