The file will be saved as YourFileName.wmf (Windows metafile). This file can be opened by Preview (on a Mac), Paint, Canvas, or similar drawing programs. Depending on the program, you can manipulate this file in numerous ways. At the very least, you should see a graphical illustration of your genome, similar to one shown in Figure 5.7. Figure . Generating a graphical output from GeneMark As we above, GeneMark is a gene prediction program, and the version embedded in DNA Master runs heuristically, using parts of the genome you enter to train the program to identify coding potential. When using the stand-alone version on the web, you can: Use an existing coding model to predict the genes. Generate a graphical output. The host profile we recommend using is that of Mycobacterium smegmatis, assuming that you used this host to isolate your phage. If you used a different host, you will obviously need to select a different bacterial profile for GeneMark. To run web-based GeneMark (we use mycobacteriophage Bongo below), go to: Also found on the Links page of Select then find and select your sequence file. This is the same ‘Browse’, YourPhage.fasta file that you imported into DNA Master. your phage’s name in the box. ‘Title’ From the dropdown box, select (assuming you ‘Species’ ’Mycobacterium_smegmatis‘ are annotating a mycobacteriophage genome). Maintain the default option of E. coli as the RBS model (there is no other). Maintain the default options for Window size, Step size, and Threshold. In the output options’ section, check each box in the first column except ‘Graphical and You PostScript graphics (email)’ putative exon splice sites’. ‘Generate ‘Mark do not need to enter an email address. Uncheck all under the output options’ heading. ‘Text Click on the GeneMark’ button at the bottom left. ‘Start Figure .
The file will be saved as YourFileName.wmf (Windows metafile). This file can be opened by Preview (on a Mac), Paint, Canvas, or similar drawing programs. Depending on the program, you can manipulate this file in numerous ways. At the very least, you should see a graphical illustration of your genome, similar to one shown in Figure 5.7. Figure . Generating a graphical output from GeneMark As we above, GeneMark is a gene prediction program, and the version embedded in DNA Master runs heuristically, using parts of the genome you enter to train the program to identify coding potential. When using the stand-alone version on the web, you can: Use an existing coding model to predict the genes. Generate a graphical output. The host profile we recommend using is that of Mycobacterium smegmatis, assuming that you used this host to isolate your phage. If you used a different host, you will obviously need to select a different bacterial profile for GeneMark. To run web-based GeneMark (we use mycobacteriophage Bongo below), go to: Also found on the Links page of Select ‘Browse’, then find and select your sequence file. This is the same YourPhage.fasta file that you imported into DNA Master. your phage’s name in the ‘Title’ box. From the ‘Species’ dropdown box, select ’Mycobacterium_smegmatis‘ (assuming you are annotating a mycobacteriophage genome). Maintain the default option of E. coli as the RBS model (there is no other). Maintain the default options for Window size, Step size, and Threshold. In the ‘Graphical output options’ section, check each box in the first column except ‘Generate PostScript graphics (email)’ and ‘Mark putative exon splice sites’. You do not need to enter an email address. Uncheck all under the ‘Text output options’ heading. Click on the ‘Start GeneMark’ button at the bottom left. Figure .
Annotation_Guide_rev.11.9.12_3.2013.docx