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  • HMM3 Search Element
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Searches each input sequence for significantly similar sequence matches to all specified HMM profiles. In case several profiles were supplied, searches with all profiles one by one and outputs united set of annotations for each sequence.

Parameters in GUI

ParameterDescriptionDefault value
Result annotationName of the result annotations.hmm_signal
SeedRandom generator seed. 0 - means that one-time arbitrary seed will be used.0
Filter by high E-valueE-value filtering can be used to exclude low-probability hits from result.1e-1
Filter by low scoreScore based filtering is an alternative to E-value filtering to exclude low-probability hits from result.0.01

Parameters in Workflow File

Type: hmm3-search

ParameterParameter in the GUIType
result-nameResult annotationstring
seqs-numNumber of seqsnumeric
scoreFilter by low scorenumeric

Input/Output Ports

The element has 2 input port. The first gets the input sequence:

Name in GUI: Input sequence

Name in Workflow File: in-sequence


Slot In GUISlot in Workflow FileType

The second input port gets the HMM profile:

Name in GUI: HMM3 profile

Name in Workflow File: in-hmm3


Slot In GUISlot in Workflow FileType
HMM profilehmm3-profilehmm3-profile

And 1 output port:

Name in GUI: HMM3 annotations

Name in Workflow File: out-annotations


Slot In GUISlot in Workflow FileType
Set of annotationsannotationsannotation-table
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