‘Bandage’ program helps stick DNA sequences back together to win 2015 iAwards
Master of Science (Bioinformatics) student Ryan Wick has won the national iAwards in the graduate student category, for his innovative software program that he has been using to analyse antibiotic resistance in bacteria, such as Salmonella.
Head of Department of Computing and Information Systems in the Melbourne School of Engineering, Professor Justin Zobel, said that Ryan’s award, which is a major national award specific to information technology, was well deserved.
“Ryan developed the software to analyse the microbial data he was gathering and showed a great deal of initiative in his minor thesis work,” Professor Zobel said.
Ryan is a student with the Holt group and was supervised by Dr Kathryn Holt and Mark Schulz from the Bio21 Institute and the Faculty of Medicine, Dentistry and Health Sciences, at the University of Melbourne and Professor Justin Zobel, from Computing and Information Systems.
For his minor thesis, he set about analysing the bacterial genome – all of its DNA – in order to find the antibiotic-resistant mutations that give it a survival advantage.
The process of DNA sequencing chops up bacterial DNA into millions of small fragments. The challenge is then to put all the fragments back together again.
Ryan used genome assembler programs which generate pages of DNA letters: Ts and As and Gs, and Cs, representing the nucleotide bases. He then went about the process of fitting them together, and trying to identify the antibiotic resistant genes.
After enquiring among his colleagues about which computer programs they used to analyse the data, he was surprised to discover that there were none.
To overcome this challenge, Ryan set about creating the program that he needed to do the job.
“I wanted to make something I could use,” he explains. ‘Bandage’ (a Bioinformatics-Application-for-Navigating-De-novo- –Assembly-Graphs-Easily) is a program that makes it possible to put the pieces back together again.
‘Bandage’ represents the assembled DNA fragments, of varying length, in a visual way and shows which sequences potentially connect to which others.
Bacterial DNA in its original form occurs in a circular chromosome. Due to the many repeats of small fragments it is not possible to reassemble a perfect circle in the exact order that it occurred in the organism, explains Ryan. However, Bandage is useful for visualising what fragments may connect to each other. It’s then up to the researcher to ‘detangle’ the fragments.
“The image created by Bandage sometimes looks a bit like a tangle of rubber bands, hence the name “Bandage”,” explains Ryan.
Interestingly, it’s in these tangles or knots of small repeated nucleotide fragments, where antibiotic resistance genes are commonly found.
“It’s a starting point that helps you know where to look,” explains Ryan. Also, there is a certain element of reproducibility of the images for sequenced genomes of particular species.
Whether it is to discover antibiotic resistant genes in bacteria, or to find unique mutations in cancer cells that cause them to metastasize, the ‘Bandage’ program provides a means of visualising genomic data, to make it possible to observe patterns and to understand how genetic sequences fit together and influence each other.
Bandage is Open Source software, that can be used and downloaded free of charge. “I am excited that researchers are already using and modifying the software for their own unique situations,” said Ryan. “I actually felt a bit out of place at the iAwards,” adds Ryan –
“this invention is free and I did not set out to make a profit.”
The iAwards recognise Australian achievements in technology innovations and are judged by the ICT industry.
View the original article, “Humpty dumpty program ‘bandage’ helps piece dna sequences back together again and wins 2015 iAwards”, by Florienne Loder and Maggie Scott, Bio21 Institute.