Hi, I tried using the GenomicFeatures package (R package) to get gene information for Salmonella enterica serovar Typhimurium SL1344 (uid86645) and Campylobacter jejuni (NCTC1168) from the UCSC genome browser,but discovered that UCSC genome browser did not have the two organisms; however, the two organisms are hosted in UCSC Microbial Genome Browser. I wonder if there is any plan to support UCSC Microbial Genome Browser in the nearest future. Thanks -- output of sessionInfo(): R version 3.0.1 (2013-05-16) Platform: x86_64-pc-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 [6] LC_MESSAGES=en_US.UTF-8 LC_PAPER=C LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] parallel stats graphics grDevices utils datasets methods base other attached packages: [1] rtracklayer_1.20.4 GenomicRanges_1.12.5 IRanges_1.18.2 lumiMouseAll.db_1.20.0 org.Mm.eg.db_2.9.0 RSQLite_0.11.4 DBI_0.2-7 [8] annotate_1.38.0 AnnotationDbi_1.22.6 limma_3.16.7 lumi_2.12.0 gplots_2.12.1 DESeq_1.12.0 lattice_0.20-24 [15] locfit_1.5-9.1 Biobase_2.20.1 BiocGenerics_0.6.0 doMC_1.3.1 iterators_1.0.6 foreach_1.4.1 loaded via a namespace (and not attached): [1] affy_1.38.1 affyio_1.28.0 beanplot_1.1 BiocInstaller_1.10.3 Biostrings_2.28.0 bitops_1.0-6 BSgenome_1.28.0 [8] caTools_1.16 codetools_0.2-8 colorspace_1.2-2 compiler_3.0.2 gdata_2.13.2 genefilter_1.42.0 geneplotter_1.38.0 [15] grid_3.0.2 gtools_3.1.0 illuminaio_0.2.0 KernSmooth_2.23-10 MASS_7.3-29 Matrix_1.1-1.1 matrixStats_0.8.5 [22] mclust_4.2 methylumi_2.6.1 mgcv_1.7-27 minfi_1.6.0 multtest_2.16.0 nleqslv_2.0 nlme_3.1-113 [29] nor1mix_1.1-4 preprocessCore_1.22.0 RColorBrewer_1.0-5 RCurl_1.95-4.1 reshape_0.8.4 R.methodsS3_1.5.2 Rsamtools_1.12.4 [36] siggenes_1.34.0 splines_3.0.2 stats4_3.0.2 survival_2.37-4 tools_3.0.2 XML_3.98-1.1 xtable_1.7-1 [43] zlibbioc_1.6.0 -- Sent via the guest posting facility at bioconductor.org.

Hi Sonia, Might just be easier to download the GFF file directly from NCBI and turn it into a TranscriptDb object with makeTranscriptDbFromGFF(). In 5 steps: 1. Pick-up your bacteria from this index: ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Bacteria/ For example Campylobacter_jejuni_NCTC_11168 in your case. 2. Click on it. 3. Download the GFF file (HE978252.gff in this case). 4. Start R, load the GenomicFeatures package and run makeTranscriptDbFromGFF() on the GFF file. If you run into problems, ?makeTranscriptDbFromGFF is your friend. 5. Let us know how it goes. Note that gene models for bacteria are so simple that putting them in a TranscriptDb object feels a little bit overkill but is sometimes needed for interoperability with some of the tools in BioC. Cheers, H. On 01/11/2014 03:33 AM, Maintainer wrote: > > Hi, > > I tried using the GenomicFeatures package (R package) to get gene information for Salmonella enterica serovar Typhimurium SL1344 (uid86645) and Campylobacter jejuni (NCTC1168) from the UCSC genome browser,but discovered that UCSC genome browser did not have the two organisms; however, the two organisms are hosted in UCSC Microbial Genome Browser. I wonder if there is any plan to support UCSC Microbial Genome Browser in the nearest future. > > Thanks > > > > -- output of sessionInfo(): > > R version 3.0.1 (2013-05-16) > Platform: x86_64-pc-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 > [6] LC_MESSAGES=en_US.UTF-8 LC_PAPER=C LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] parallel stats graphics grDevices utils datasets methods base > > other attached packages: > [1] rtracklayer_1.20.4 GenomicRanges_1.12.5 IRanges_1.18.2 lumiMouseAll.db_1.20.0 org.Mm.eg.db_2.9.0 RSQLite_0.11.4 DBI_0.2-7 > [8] annotate_1.38.0 AnnotationDbi_1.22.6 limma_3.16.7 lumi_2.12.0 gplots_2.12.1 DESeq_1.12.0 lattice_0.20-24 > [15] locfit_1.5-9.1 Biobase_2.20.1 BiocGenerics_0.6.0 doMC_1.3.1 iterators_1.0.6 foreach_1.4.1 > > loaded via a namespace (and not attached): > [1] affy_1.38.1 affyio_1.28.0 beanplot_1.1 BiocInstaller_1.10.3 Biostrings_2.28.0 bitops_1.0-6 BSgenome_1.28.0 > [8] caTools_1.16 codetools_0.2-8 colorspace_1.2-2 compiler_3.0.2 gdata_2.13.2 genefilter_1.42.0 geneplotter_1.38.0 > [15] grid_3.0.2 gtools_3.1.0 illuminaio_0.2.0 KernSmooth_2.23-10 MASS_7.3-29 Matrix_1.1-1.1 matrixStats_0.8.5 > [22] mclust_4.2 methylumi_2.6.1 mgcv_1.7-27 minfi_1.6.0 multtest_2.16.0 nleqslv_2.0 nlme_3.1-113 > [29] nor1mix_1.1-4 preprocessCore_1.22.0 RColorBrewer_1.0-5 RCurl_1.95-4.1 reshape_0.8.4 R.methodsS3_1.5.2 Rsamtools_1.12.4 > [36] siggenes_1.34.0 splines_3.0.2 stats4_3.0.2 survival_2.37-4 tools_3.0.2 XML_3.98-1.1 xtable_1.7-1 > [43] zlibbioc_1.6.0 > > -- > Sent via the guest posting facility at bioconductor.org. > > ____________________________________________________________________ ____ > devteam-bioc mailing list > To unsubscribe from this mailing list send a blank email to > devteam-bioc-leave at lists.fhcrc.org > You can also unsubscribe or change your personal options at > https://lists.fhcrc.org/mailman/listinfo/devteam-bioc > -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpages at fhcrc.org Phone: (206) 667-5791 Fax: (206) 667-1319