{"data":{"id":"10.6084/m9.figshare.782261","type":"dois","attributes":{"doi":"10.6084/m9.figshare.782261","prefix":"10.6084","suffix":"m9.figshare.782261","identifiers":[],"alternateIdentifiers":[],"creators":[{"name":"Reumerman, Richard A.","nameType":"Personal","givenName":"Richard A.","familyName":"Reumerman","affiliation":[],"nameIdentifiers":[]},{"name":"Tucker, Nicholas P.","nameType":"Personal","givenName":"Nicholas P.","familyName":"Tucker","affiliation":[],"nameIdentifiers":[]},{"name":"Herron, Paul R.","nameType":"Personal","givenName":"Paul R.","familyName":"Herron","affiliation":[],"nameIdentifiers":[]},{"name":"Hoskisson, Paul A","nameType":"Personal","givenName":"Paul A","familyName":"Hoskisson","affiliation":[],"nameIdentifiers":[{"schemeUri":"https://orcid.org","nameIdentifier":"https://orcid.org/0000-0003-4332-1640","nameIdentifierScheme":"ORCID"}]},{"name":"Vartul Sangal","affiliation":[],"nameIdentifiers":[]}],"titles":[{"title":"Tool for rapid annotation of microbial SNPs (TRAMS): a simple program for rapid annotation of genomic variation in prokaryotes."}],"publisher":"figshare","container":{},"publicationYear":2013,"subjects":[{"subject":"Computational Biology"},{"subject":"60102 Bioinformatics","subjectScheme":"FOR"},{"subject":"FOS: Computer and information sciences","schemeUri":"http://www.oecd.org/science/inno/38235147.pdf","subjectScheme":"Fields of Science and Technology (FOS)"},{"subject":"FOS: Computer and information sciences","subjectScheme":"Fields of Science and Technology (FOS)"},{"subject":"Genetics"},{"subject":"FOS: Biological sciences","schemeUri":"http://www.oecd.org/science/inno/38235147.pdf","subjectScheme":"Fields of Science and Technology (FOS)"},{"subject":"FOS: Biological sciences","subjectScheme":"Fields of Science and Technology (FOS)"},{"subject":"Microbiology"},{"subject":"Evolutionary Biology"}],"contributors":[],"dates":[{"date":"2013-08-27","dateType":"Created"},{"date":"2015-12-02","dateType":"Updated"},{"date":"2013","dateType":"Issued"}],"language":null,"types":{"ris":"DATA","bibtex":"misc","citeproc":"dataset","schemaOrg":"Dataset","resourceType":"Dataset","resourceTypeGeneral":"Dataset"},"relatedIdentifiers":[],"relatedItems":[],"sizes":["129251992 Bytes"],"formats":[],"version":null,"rightsList":[{"rights":"Creative Commons Attribution 4.0 International","rightsUri":"https://creativecommons.org/licenses/by/4.0/legalcode","schemeUri":"https://spdx.org/licenses/","rightsIdentifier":"cc-by-4.0","rightsIdentifierScheme":"SPDX"}],"descriptions":[{"description":"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). \u003cstrong\u003ePlease cite\u003c/strong\u003e Reumerman, R. A., Tucker, N. P., Herron, P. R., Hoskisson, P. A., \u0026amp; 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 http://link.springer.com/article/10.1007%2Fs10482-013-9953-x UPDATED 24th September 2013 see Changelog.txt ==[Version1.0.2]== 130923:Fixed issue where program crashed on absence of certain features in genbank file. ==[Version1.0.1]== 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 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