| 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:
- 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
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