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An explanation of the fields and options in the SNAP submission page:
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| E-mail field |
E-mail is required. Please make sure that there are no typos -- e-mail is the only way we can report your results if you close the browser window |
| Entry Name |
Name of the request being submitted (NOTE: this field is NOT filtered). Please avoid using the same name for multiple requests.
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| Sequence format |
Default: simple sequence format in one letter amino-acid code. No characters except letters, returns, and spaces allowed
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| Mutant format |
Mutations that require SNAP predictions should be reported in format XposY in the Input Substitutions field.
Example: Substitution of valine by isoleucine in position 36 of the sequence should be entered as V36I
When submitting multiple single mutants separate them by commas
In silico mutagenesis requests can be made in the subset of regular expression format using the Input substitutions pattern field and hitting the Generate Mutants button.
- Mutants should be in format XposY, where X is the wild-type amino acid, pos is the position in sequence, and Y is the mutant
- X is not required, and Y and pos can be replaced by a star (*)
- Possibilities of patterns include:
- ** = Substitute all residues in sequence by all other residues
- *Y = Substitute all residues in sequence by residue Y (residue scans, i.e. alanine scanning)
- pos* = Substitute the residue in position pos by all other residues
- posY = Substitute the residue in position pos by residue Y (NOTE: this is equivalent to actually writing out the corresponding substitution)
- X** = Substitute all residues X in sequence by all other residues
- X*Y = Substitute all residues X in sequence by residue Y
- Xpos* = Substitute residue X in position pos by all other residues
- XposY = Substitue residue X in position pos by residue Y (NOTE: this is equivalent to posY and to simply putting the same substitution into the subs field)
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| Min reliability index |
SNAP will report only predictions with relibility indices higher than set minimum, default=0 (all are reported)
Reliability indices (RI's) are indicative of confidence in prediction. They are also directly related to expected accuracy.
For more information on this topic please see the graph below and/or read the referenced paper
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| Min expected accuracy |
SNAP will only report predictions that are made with at least this level of accuracy, default=50%
Expected accuracy is a number of correctly predicted (at a given reliability index) neutral or non-neutral samples in the SNAP testing set
This measure of accuracy is meant to illustrate the likelihood that a given prediction is correct
For more information on this topic please see the graph below and/or read the referenced paper |
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If you find SNAP useful for your research, please cite:
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Bromberg Y & Rost B. SNAP: predict effect of non-synonymous polymorphisms on function. Nucleic Acids Research, 2007, Vol. 35, No. 11 3823-3835 PubMed PDF
SNAP RostLab Contact
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