1. Converting DNA Sequence file formats with BioPython
Tolulope Perrin-Stowe Program in Ecology, Evolution, and Conservation Biology
Why convert sequence files?
How to create a file conversion code
There are many different bioinformatics programs that can be used to run analyzes on DNA sequences. Several are typically used in one publication. These programs can require a variety of different input file formats. The three file formats most often used in my research are Fasta, PHYLIP, and NEXUS files. Converting between these file formats often requires several additional programs when working in Windows. This can make keeping track of the many file outputs with different formats difficult.
This code was written in BioPython, which uses Python coding to create tools for computational molecular biology. BioPython is freely available along with tutorials and packages that were used to write this code. The code takes either a Fasta file or a Genbank file (common sequence format file types) as an input and can convert the Fasta file into either a NEXUS or a PHYLIP file after using the program MUSCLE to first align the sequences. The Genbank file can be directly converted into a Fasta file.
Fasta file
Genbank file
Code aligns sequence file using MUSCLE
NEXUS file
PHYLIP file
Input
Output or
Sequence file conversion code
Acknowledgements
Citations
I would like to thank Halie Rando, Kelsey Witt, Diana Byrne, Alya Stein, and Heidi Imker for their help in completion of this project and for their work in the course.
Cock, P., Antao ,T., Chang, J. T., Chapman, B.A. , Cox, C.J. , Dalke, A., Friedberg, I., Hamelryck, T, Kauff, F. , Wilczynski, B. , and de Hoon, M. J. L. (2009). Biopython: freely available Python tools for computational molecular biology and
bioinformatics. Bioinformatics. 25 (11): doi: /bioinformatics/btp163
Edgar, R.C. (2004). MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucl. Acids Res. 32 (5): doi: /nar/gkh340
This work was part of a Focal Point grant funded by the Graduate College at the University of Illinois at Urbana-Champaign