A team of researchers at Bangladesh Agricultural University (BAU) has built software that measures how similar DNA sequences are quickly and with little computing power. The researchers say a comparison that can take about a month by manual methods takes a few seconds with the new tool. It is free to use in both desktop and web versions; the web version is at dnasimlab.com.
The software was presented on Monday (2 November) at a workshop in the conference room of the dean of BAU's Faculty of Agricultural Engineering and Technology. The team was led by Dr Mesbah Uddin, associate professor of Computer Science and Mathematics (CSM). It also included Maifi-Ul Asad and two undergraduate students of bioinformatics engineering, Muhammad Ishmamul Haque and Md Asifuzzaman. The work was supported by the government's ICT Division.
The researchers explained the method. Rather than matching two DNA sequences letter by letter, they take short fragments of one sequence and check how often they occur in the other. Because the letters on DNA's two strands come in pairs (A-T, C-G), reverse-pair matches are counted as well as direct ones. This produces a list of numbers for each sequence, and comparing those lists gives a phylogenetic tree, the family tree of the sequences.
In tests, trees built this way were 95 to 100 per cent accurate. The tool ran 55 to 1,747 times faster than MEGA, a widely used program, and used 30 to 99 per cent less memory than other methods. A paper on the research has been published in the international journal Molecular Genetics and Genomics.
The faculty dean, Professor Dr Abdul Mazid, was chief guest, and the head of the CSM department, Md Sayed Iftikhar Yousuf, chaired the workshop. The dean said the user-friendly software, the result of three months of intensive work, was a real achievement in both its use and its presentation. Those present said they hoped it would open new ground for bioinformatics research and software development in Bangladesh.
The story was reported by Barta24's BAU correspondent.
Photo: Ibrahim Husain Meraj / Wikimedia Commons (CC BY-SA 4.0)
Source: Barta24
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