Tool for rapid annotation of microbial SNPs (TRAMS): a simple program for rapid annotation of genomic variation in prokaryotes.
Datasets usually provide raw data for analysis. This raw data often comes in spreadsheet form, but can be any collection of data, on which analysis can be performed.
TRAMS (Tool for Rapid Annotation of Microbial SNPs) is a program 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 only a tab delimited text file containing SNP locations, reference nucleotide and SNPs in different strains along with a reference genome sequence in standard GenBank or EMBL format. TRAMS annotates SNPs as synonymous, non-synonymous or nonsense. Non-synonymous SNPs in start and stop codons are separated as non-start and non-stop SNPs, respectively. SNPs in overlapping features are annotated separately for each feature and multiple nucleotide polymorphisms (MNPs) within a codon are combined prior to annotation.
We have also developed a workflow for use in Galaxy 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.
Availability: TRAMS is available here to download as Python script and single file executable for WINDOWS and also in the Galaxy tool shed (http://toolshed.g2.bx.psu.edu/view/rreumerman/snptools).
Reumerman, R. A., Tucker, N. P., Herron, P. R., Hoskisson, P. A., & Sangal, V. (2013). 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. doi:10.1007/s10482-013-9953-x
The full published manuscript is available
UPDATED 24th September 2013 see Changelog.txt
130923:Fixed issue where program crashed on absence of certain features in genbank file.
130919:Fixed issue where'Gene'and'Source' were not recognized as'gene'and'source'.
130919:Fixed issue where features' strands were mysteriously no longer recognized if on +1 strand.