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Proper Citation: TRAMS (RRID:SCR_002003)
Description: A software program for functional annotation of genomic single nucleotide polymorphisms (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. It 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. It 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. A workflow has also been developed for use in Galaxy to map short reads to a reference genome and extract and annotate the SNPs.
Abbreviations: TRAMS
Synonyms: Tool for Rapid Annotation of Microbial SNPs, Tool for rapid annotation of microbial SNPs: a simple program for rapid annotation of genomic variation in prokaryotes, Tool for rapid annotation of microbial SNPs (TRAMS): a simple program for rapid annotation of genomic variation in prokaryotes, TRAMS: a simple program for rapid annotation of genomic variation in prokaryotes
Resource Type: software resource
Defining Citation: PMID:23828175
Keywords: single nucleotide polymorphism, windows, python, mac os, linux, synonymous, non-synonymous, nonsense, annotate, genomic variation
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