无忧视频

HMC Biologists Develop New Software

Sometimes writing software is like any other kind of writing; it takes a few drafts to get it right, but the final result is worth the extra effort. 无忧视频 Biology Professor Eliot Bush knows that feeling. His recently released software program, xenoGI, which helps researchers reconstruct the history of genomic island insertions in clades of closely related microbes, didn鈥檛 exactly happen overnight. 鈥淲e started it more than five years ago,鈥� he says. 鈥淲e had students working on it already in 2012. So it鈥檚 been percolating for a while. In summer 2016, I started to get more serious about it, and rewrote the system from scratch, and added a number of new features.鈥�

A paper describing the project, 鈥渪enoGI: Reconstructing the history of genomic island insertions in clades of closely related bacteria鈥� was published by BMC Bioinformatics Feb. 5. The team鈥� Bush, Anne聽Clark 鈥�13, Carissa聽DeRanek 鈥�19, Alexander聽Eng, Juliet聽Forman 鈥�18, Kevin聽Heath 鈥�16, Alexander聽Lee 鈥�14, biology professor Daniel Stoebel, Zunyan聽Wang 鈥�18, Matthew聽Wilber 鈥�17聽and Helen聽Wu 鈥�12鈥攈as made the so that others can use it and help work out any bugs.

While studying how bacteria regulate themselves genetically, Harvey Mudd biology researchers couldn鈥檛 find software to handle the scope of their work, so they decided to write their own.

鈥淭his really came out of Dan Stoebel鈥檚 research interests,鈥� Bush says. Stoebel studies gene regulation in bacteria and was interested in studying the regulation of genes arriving in genomic islands. Genomic islands are clusters of genes that have entered a genome via horizontal transfer, that is, outside of the normal method of parent-offspring inheritance. Stoebel hoped to research a large clade of E. coli bacteria, but existing software packages didn鈥檛 look at a species鈥� whole evolutionary history in this way. So, Bush developed a software package that helps users understand the adaptive path that has produced specific living species.

鈥淓very gene in that group has one of two origins,鈥� says Bush. 鈥淓ither it was present in the common ancestor of those species, or it entered the group in a horizontal transfer event. The goal of the software is to distinguish these two things, for all the genes in each strain.鈥� The ability to identify the history of genomic island insertions in a clade of bacteria makes xenoGI novel compared to previous software programs.

Genomic islands play a broad role in microbial genome evolution, providing a mechanism for strains to adapt to new ecological conditions. 鈥淴enoGI is an effective tool for studying the history of genomic island insertions because it identifies genomic islands and determines which branch they inserted on within the phylogenetic tree for the clade,鈥� says Bush.

So far, Bush is pleased with the response he鈥檚 received from people using xenoGI, and there has been a fair amount of traffic on the Github page.

Bush believes the program holds potential to improve other areas of research, including whole genome alignment between bacteria. 鈥淎lignment involves figuring out which parts of one sequence correspond to which parts of another one,鈥� he says. 鈥淭hese days it鈥檚 possible to make alignments between whole genomes, and many kinds of researchers make use of such alignments. I think a lot of the stuff xenoGI figures out in the process of doing its thing could be very useful for the whole genome alignment problem.鈥�