| Name | Modified | Size | Downloads / Week |
|---|---|---|---|
| FEATnotator_1.1.3.tar.gz | 2018-06-01 | 83.0 MB | |
| README | 2018-05-31 | 2.3 kB | |
| FEATnotator_Manual.pdf | 2018-05-31 | 567.3 kB | |
| FEATnotator_1.1.2.tar.gz | 2015-04-06 | 83.0 MB | |
| FEATnotator_1.1.1.tar.gz | 2015-03-26 | 83.0 MB | |
| FEATnotator_1.1.0.tar.gz | 2015-02-01 | 83.0 MB | |
| Totals: 6 Items | 332.5 MB | 0 |
1. Downloading the Software FEATnotator software is available for download from the sourceforge project website, http://featnotator.sourceforge.net. Download the file FEATnotator_1.1.3.tar.gz and save it locally on your computer. Extract the contents using the tar command. $ tar -xvzf FEATnotator_1.1.3.tar.gz $ cd FEATnotator $ ls README bin docs example 2. Prerequisites for FEATnotator FEATnotator software is written completely in standard Perl. So, once you download and extract the contents of the tar.gz file, the software would be ready for execution on most of the standard computers. The software was developed and tested on Ubuntu 12.04.4 LTS and Mac OS X 10.8. It is run through command line interface. FEATnotator optionally generates graphical content summarizing the annotation results, for which it requires an installation of R (http://www.r-project.org). 3. Components The downloaded package of FEATnotator software has three sub folders: bin, docs and example. 3.1. Scripts The bin folder contains two perl scripts: i. FEATnotator.pl This is the primary script that integrates the user supplied input features with overlapping and proximal reference annotation features. It optionally generates pie charts showing the distribution of the input features over the genome with reference to the annotated genes. ii. plotFeatureDistribution.pl This additional script computes the distribution of the input features within a specified chromosomal region into sliding windows of custom width and displays it as a line graph. For SNP features supplied as input, it also marks the distribution of Nonsense and Missense SNPs along with those overlapping with the splice sites of the coding genes. 3.2. Documentation The docs folder comprises of this user manual. 3.3. Examples The example folder contains the genomic variation data from Arabidopsis thaliana ecotype WS obtained from http://mus.well.ox.ac.uk/19genomes/ (Gan et al., 2011). The data illustrates the use of FEATnotator in the context of annotating SNPs, indels and marker information (see section 6, Case Studies). Reference annotation information along with the genome sequence from Arabidopsis thaliana TAIR10 (http://www.arabidopsis.org) is also provided. For more details view the FEATnotator_Manual.pdf from docs.