Tool for rapid annotation of microbial SNPs (TRAMS): a simple program for rapid annotation of genomic variation in prokaryotes
| Autor: | Nicholas P. Tucker, Paul Herron, Paul A. Hoskisson, Vartul Sangal, Richard Reumerman |
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| Rok vydání: | 2013 |
| Předmět: |
Genetics
Nonsynonymous substitution Computational Biology High-Throughput Nucleotide Sequencing General Medicine Computational biology Biology Microbiology Polymorphism Single Nucleotide Stop codon DNA sequencing SNP genotyping Access to Information Annotation Prokaryotic Cells SNP annotation GenBank Molecular Biology Reference genome |
| DOI: | 10.6084/m9.figshare.790665.v1 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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