Abstract
Next generation sequencing (NGS) has been widely used to study genomic variation in a variety of prokaryotes. Single nucleotide polymorphisms (SNPs) resulting from genomic comparisons need to be annotated for their functional impact on the coding sequences. We have developed a program, TRAMS, for functional annotation of genomic SNPs which is available to download as a single file executable for WINDOWS users with limited computational experience and as a Python script for Mac OS and Linux users. TRAMS needs a tab delimited text file containing SNP locations, reference nucleotide and SNPs in variant strains along with a reference genome sequence in GenBank or EMBL format. SNPs are annotated as synonymous, nonsynonymous or nonsense. Nonsynonymous SNPs in start and stop codons are separated as non-start and non-stop SNPs, respectively. SNPs in multiple overlapping features are annotated separately for each feature and multiple nucleotide polymorphisms within a codon are combined before annotation. We have also developed a workflow for Galaxy, a highly used tool for analysing NGS data, to map short reads to a reference genome and extract and annotate the SNPs. TRAMS is a simple program for rapid and accurate annotation of SNPs that will be very useful for microbiologists in analysing genomic diversity in microbial populations.
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Acknowledgments
This study was supported by Medical Research Scotland Grant 422 FRG to Paul A. Hoskisson. Richard A. Reumerman was funded by a SULSA studentship awarded to Paul R. Herron.
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TRAMS is available to download as Python script and single file executable for WINDOWS from http://sourceforge.net/projects/strathtrams/files/Latest/ and also in the Galaxy tool shed (http://toolshed.g2.bx.psu.edu/view/rreumerman/snptools).
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Reumerman, R.A., Tucker, N.P., Herron, P.R. et al. Tool for rapid annotation of microbial SNPs (TRAMS): a simple program for rapid annotation of genomic variation in prokaryotes. Antonie van Leeuwenhoek 104, 431–434 (2013). https://doi.org/10.1007/s10482-013-9953-x
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DOI: https://doi.org/10.1007/s10482-013-9953-x