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Passta - Manual

Sequence Format:

Passta supports sequences in FASTA format via file upload or copy&paste in a textfield. A sequence in FASTA format begins with a single-line description, followed by lines of sequence data. Passta doesn't accept multi-sequences.
  • The description line starts with a greater than symbol (">").
  • The word following the greater than symbol (">") immediately is the "ID" (name) of the sequence, the rest of the line is the description.
  • The "ID" and the description are optional.
  • all lines of text should be shorter than 80 (normally 60) characters.
The following example contains one sequence (sequence_1):
    >sequence_1
    GLAKDAWEIPRESLRLEAKLGQGCFGEVWMGTWNDTTRVAIKTLKPGTMSPEAFLQEAQVMKKLRHEKLVQLYAV
    VSEEPIYIVIEYMSKGSLLDFLKGEMGKYLRLPQLVDMAAQIASGMAYVERMNYVHRDLRAANILVGENLVCKVA
    DFGLARLIEDNEYTARQGAKFPIKWTAPEAALYGRFTIKSDVWSFGILLTELTTKGRVPYPGMVNREVLDQVERG
    YRMPCPPECPESLHDLMCQCWRKDPEERPTFKYLQAQLLPACVLEVAE

Parameter Description:

Passta is a program with many parameters. They can be separated in global parameters, "Pass One" (the heuristic filter), and "Pass Two" (annotation) parameters. Currently, only some of them may be changed by the user. These are:

Global parameters:

Mode:
Set Passta working mode

mode description
0 fast (less sensitive)
1 normal (default)
2 sensitive (rather slow in Pass Two)

Secondary structure profile:
If checked, Passta will compute a secondary structure profile.

Pass Two: Annotation parameters

Jump cost:
specify jumpcost for Pass Two annotation. The default values are good for the BLOSUM62 substitution matrix. You can provide three values to generate a Jumpcost function for Passta:

value
Start 36
Stop 43
Step 6

will generate a function whose output is 36, 42.

Rearrangement cost:
specify rearrangement cost for Pass Two annotation. The default values are good for the BLOSUM62 substitution matrix. You can provide three values to generate a Rearrangement cost function for Passta:

value
Start 34
Stop 37
Step 2

will generate a function whose output is 34, 46.

Deletion cost:
specify deletion cost for Pass Two annotation. The default value (Default: 20) is good for the BLOSUM62 substitution matrix.

Note: Keep the number of values emitted by the jumpcost and rearrangement cost functions low! Both functions are combined in Passta, such that the above examples yield results for the following combinations:

JC RC DC
1. 36 34 20
2. 36 36 20
3. 42 34 20
4. 42 36 20
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Fri Dec 14 12:59:41 2012