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Export all protein sequences from a genome
| Link to this post | posted 24 Sep, 2015 19:51 | |
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Is there a way to export the protein sequences in a single file (fasta format) for all the genes of a phage using DNA Master? Or, is there another way that I can get that info? Thanks for your help! |
| Link to this post | posted 24 Sep, 2015 19:52 | |
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In DNA Master: 1. DNA Menu, bottom item is "Save ORF's…" which will bring up the tool window 2. You will see a list of all the features in your phage 3. Select one or more by clicking, or use the "Select all genes" button 4. Go to the "Specify Export Files" tab 5. Use the checkboxes as appropriate to control what will be saved (e.g. "Peptide Sequences"  6. Click the "Save" button |
| Link to this post | posted 24 Sep, 2015 19:57 | |
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Thanks Chris! |
| Link to this post | posted 24 Sep, 2015 19:58 | |
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You can also do this in Phamerator: 1. Click "Phages" 2. Highlight your phage in the list 3. From the File menu, "Export Proteins (fasta)" |
| Link to this post | posted 24 Sep, 2015 19:59 | |
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The fasta file from either source will work as input for another program but it can be a hassle if you want to see the sequences yourself. In that case you will probably want to reformat. On the web I use the EMBOSS tool called seqret to do that. Do a google search on "emboss seqret ebi" and pick the seqret server at www.ebi.ac.uk You can upload your fasta file and select "FASTA format" as the output format and all the sequences will be formatted so you can see the entire protein sequence without having to do so much horizontal scrolling. |