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Finds similar protein sequence using remote BLAST. Using IDs of sequences found loads annotation for DAS sources. Nucleotide sequences are skipped if any supplied to input.

Parameters in GUI

ParameterDescriptionDefault value
Max result IDsUse first IDs of similar sequences to load annotations.5
DatabaseDatabase against which the search is performed: UniProtKB or clusters of sequences with 100%, 90% or 50% identity.UniProtKB
Min identityMinimum identity of a BLAST result and an input sequence. 90%
ThresholdThe expectation value (E) threshold is a statistical measure of the number of expected matches in a random database. The lower the e-value, the more likely the match is to be significant.10
MatrixThe matrix assigns a probability score for each position in an alignment.Auto
FilteringLow-complexity regions (e.g. stretches of cysteine in Q03751, or hydrophobic regions in membrane proteins) tend to producespurious, insignificant matches with sequences in the database which have the same kind of low-complexity regions, but are unrelated biologically. If 'Filter low complexity regions' is selected, the query sequence will be run through the program SEG, and all amino acids in low-complexity regions will be replaced by X's.None
GappedThis will allow gaps to be introduced in the sequences when the comparison is done.true
HitsLimits the number of returned alignments.250
Feature sourcesThe DAS sources to read features from.InterPro-Matches-Overview, Pride DAS 1.6, UniProt, cbs_sort, signalp

Parameters in Workflow File

Type: dasannotation-search

ParameterParameter in the GUIType
idsnumberMax result IDsnumeric
dbDatabasestring
identityMin identity

numeric

thresholdThresholdstring
matrixMatrixstring
filteringFilteringstring
gappedGappedstring
maxresHitsstring
fsourcesFeature sourcesstring

Input/Output Ports

The element has 1 input port:

Name in GUI: Input sequences

Name in Workflow File: in-sequence

Slots:

Slot In GUISlot in Workflow FileType
Sequencesequencestring

The element has 1 output port:

Name in GUI: DAS annotations

Name in Workflow File: out-annotations

Slots:

Slot In GUISlot in Workflow FileType
Set of annotationsannotationsannotation-table-list

 

 

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