Dr Catherine Putonti is co-author of ‘MiIP: The Monomer Identification and Isolation Program’, recently published in Evolutionary Bioinformatics.  We asked Dr Putonti to tell us about the background to the paper.

To start please tell us about the genesis of your paper. Why did you consider it to be important that it should be written? How does it advance existing knowledge in the field?

It was never going to be easy analyzing the evolutionary relationships within the largest collection of alpha satellite monomers ever assembled (several hundred KBs worth of sequence) and without a program to assist in the effort, it was likely an impossible task. Several programs did exist, but none had both the options we wanted for analyzing our sequences and the ability to produce output we could easily import into other applications, especially phylogenetic analyses. This was the inspiration for MiIP, although, as we ultimately discovered, going from concept to reality would prove more difficult than we imagined.

When writing a paper what challenges do you face? How did these challenges impact this particular paper? Is there anything you plan to do differently in the future to avoid them?

There was a two-fold challenge we faced in developing MiIP for the analysis of alpha satellite monomers. Firstly, there is extreme degeneracy in the monomeric sequences. Secondly, the alpha satellite sequences are amidst numerous other short repetitive elements. Given these two challenges, a robust solution had to be developed that was capable of minimizing false positive results while maintaining a high sensitivity to variants.

Why did you choose to submit it to this journal? What qualities of the journal did you find particular appealing? How long have you been aware of the journal? Did publishing a paper in the journal alter your view of it?

The MiIP software tool was developed to assist our ongoing sequencing and annotation of centromeric DNA. In particular, we wished to facilitate our analysis of the evolutionary relationships within the wide variety of alpha satellite sequences found on the same or different chromosomes. Evolutionary Bioinformatics was a perfect fit for our application as the journal is read by a wide audience including other persons studying the evolution of monomeric sequences and those in the wider area of evolutionary biology examining the variety of repetitive elements.

What is your opinion of other papers recently published within the subject are of your paper? What do you think their strengths and weaknesses (if any) are?

MiIP is a unique tool, developed for the difficult task of analyzing the evolution of repetitive elements. While there are a number of tools available for the analysis of repetitive elements (DNA as well as protein), none of them performed well for our monomeric sequences. MiIP provides a new tool, expanding the current arsenal of programs for studying repetitive elements.

How has the writing of this paper and its underlying research changed or developed your views or understanding of the field? How has this affected your future research plans?

The development of MiIP was essential to the analysis of monomeric alpha satellite sequences within the centromeric regions of several human chromosomes. Analysis of these sequences with MiIP has uncovered several evolutionarily significant and unexpected relationships that we are now examining in greater detail in order to provide a more complete description of the evolution of human centromeric regions.

Visit Dr Putonti's webpage here: www.putonti-lab.com

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