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Passta - Manual
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.
>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:
Secondary structure profile: Pass Two: Annotation parametersJump
cost:
will generate a function whose output is 36, 42. Rearrangement cost:
will generate a function whose output is 34, 46. Deletion cost: 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:
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