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. Harvey Mudd College 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\u2019t exactly happen overnight. \u201cWe started it more than five years ago,\u201d he says. \u201cWe had students working on it already in 2012. So it\u2019s 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.\u201d<\/p>\n
A paper describing the project, \u201cxenoGI: Reconstructing the history of genomic island insertions in clades of closely related bacteria\u201d was published by BMC Bioinformatics Feb. 5. The team\u2014 Bush, Anne\u00a0Clark \u201913, Carissa\u00a0DeRanek \u201919, Alexander\u00a0Eng, Juliet\u00a0Forman \u201918, Kevin\u00a0Heath \u201916, Alexander\u00a0Lee \u201914, biology professor Daniel Stoebel, Zunyan\u00a0Wang \u201918, Matthew\u00a0Wilber \u201917\u00a0and Helen\u00a0Wu \u201912\u2014has made the code available on Github<\/a> so that others can use it and help work out any bugs.<\/p>\n While studying how bacteria regulate themselves genetically, Harvey Mudd biology researchers couldn\u2019t find software to handle the scope of their work, so they decided to write their own.<\/p>\n \u201cThis really came out of Dan Stoebel\u2019s research interests,\u201d 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\u2019t look at a species\u2019 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.<\/p>\n \u201cEvery gene in that group has one of two origins,\u201d says Bush. \u201cEither 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.\u201d The ability to identify the history of genomic island insertions in a clade of bacteria makes xenoGI novel compared to previous software programs.<\/p>\n Genomic islands play a broad role in microbial genome evolution, providing a mechanism for strains to adapt to new ecological conditions. \u201cXenoGI 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,\u201d says Bush.<\/p>\n So far, Bush is pleased with the response he\u2019s received from people using xenoGI, and there has been a fair amount of traffic on the Github page.<\/p>\n Bush believes the program holds potential to improve other areas of research, including whole genome alignment between bacteria. \u201cAlignment involves figuring out which parts of one sequence correspond to which parts of another one,\u201d he says. \u201cThese days it\u2019s 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.\u201d<\/p>\n","protected":false},"excerpt":{"rendered":" Sometimes writing software is like any other kind of writing; it takes a few drafts to get it right, but […]<\/p>\n","protected":false},"author":145,"featured_media":6334,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"_acf_changed":false,"footnotes":""},"categories":[4,11,14,30],"class_list":["post-6332","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-biology","category-computer-science","category-faculty","category-students"],"acf":[],"_links":{"self":[{"href":"https:\/\/www.hmc.edu\/about\/wp-json\/wp\/v2\/posts\/6332","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.hmc.edu\/about\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.hmc.edu\/about\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.hmc.edu\/about\/wp-json\/wp\/v2\/users\/145"}],"replies":[{"embeddable":true,"href":"https:\/\/www.hmc.edu\/about\/wp-json\/wp\/v2\/comments?post=6332"}],"version-history":[{"count":0,"href":"https:\/\/www.hmc.edu\/about\/wp-json\/wp\/v2\/posts\/6332\/revisions"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/www.hmc.edu\/about\/wp-json\/wp\/v2\/media\/6334"}],"wp:attachment":[{"href":"https:\/\/www.hmc.edu\/about\/wp-json\/wp\/v2\/media?parent=6332"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.hmc.edu\/about\/wp-json\/wp\/v2\/categories?post=6332"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}