title: Tool for rapid annotation of microbial SNPs (TRAMS): a simple program for rapid annotation of genomic variation in prokaryotes.
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.
authors.affiliation: Strathclyde Institute of Pharmacy and Biomedical Sciences, 161 Cathedral Street, Glasgow, UK.
authors.forename: Richard A
authors.initials: RA
authors.lastname: Reumerman
authors.forename: Nicholas P
authors.initials: NP
authors.lastname: Tucker
authors.forename: Paul R
authors.initials: PR
authors.lastname: Herron
authors.forename: Paul A
authors.initials: PA
authors.lastname: Hoskisson
authors.forename: Vartul
authors.initials: V
authors.lastname: Sangal
mesh_terms: D022126:Access to Information; D019295:Computational Biology / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing; D020641:Polymorphism, Single Nucleotide; D011387:Prokaryotic Cells