Abie Pro 3.0 Demo Help: Peptide Antibody Design

Frequently Asked Questions:

1. Why can't I paste in my sequences?
To copy and paste your sequences into the input windows of Abie, you may need to use Control(Ctrl)+c or Apple+c for copy, and Control(Ctrl)+v or Apple+v for paste. To copy, highlight the sequences and press simultaneously the Control(Ctrl) and the c keys. To paste, first mouse click in the input window, then press simultaneously the Control(Ctrl) and the v keys.

Mac OSX 10 IE5.1 has a bug, it does not allow copy/paste into a Java text field, thus you will not be able to import a new sequence. Attempting copy/paste may kill your browser. Later Mac IE versions should work fine. Stand-only version of Abie does not use IE, so copy/paste works fine.

2. What input sequence formats does Abie accept?

Abie accepts sequences in the single-letter codes. It will discard any nubmers and white spaces. As long as your sequences contain no letters that don't represent the 20 amino acids, it shall work fine.

3. I pasted in a sequence, and clicked on go, but nothing happened.
Abie will silently discard any numbers and white spaces in the input sequences, but will not discard letters that don't represent any amino acids. If your sequence contains non-amino acid letters such as "X", the program will terminate without returning any results.
4. My protein is a mouse protein, do I need the stand-only version?
You don't need the stand-only version if you don't want to use the "Avoid cross-reactions" option. If your protein is a mouse protein, you can use the free Abie online. If your protein is of a species that is a close relative of mouse, you may also use the online version (For best results, the stand-only version is suggested). Please check the User Instructions for details.
5. Can I use Abie for designing a fusion protein to raise an antibody?
The maximum peptide length allowed for Abie is 199. You could produce a long peptide by express it as a fusion protein.

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