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
| Parameter | Description | Default value |
|---|---|---|
| Max result IDs | Use first IDs of similar sequences to load annotations. | 5 |
| Database | Database against which the search is performed: UniProtKB or clusters of sequences with 100%, 90% or 50% identity. | UniProtKB |
| Min identity | Minimum identity of a BLAST result and an input sequence. | 90% |
| Threshold | The 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 |
| Matrix | The matrix assigns a probability score for each position in an alignment. | Auto |
| Filtering | Low-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 |
| Gapped | This will allow gaps to be introduced in the sequences when the comparison is done. | true |
| Hits | Limits the number of returned alignments. | 250 |
| Feature sources | The DAS sources to read features from. | InterPro-Matches-Overview, Pride DAS 1.6, UniProt, cbs_sort, signalp |
Parameters in Workflow File
Type: dasannotation-search
| Parameter | Parameter in the GUI | Type |
|---|---|---|
| idsnumber | Max result IDs | numeric |
| db | Database | string |
| identity | Min identity | numeric |
| threshold | Threshold | string |
| matrix | Matrix | string |
| filtering | Filtering | string |
| gapped | Gapped | string |
| maxres | Hits | string |
| fsources | Feature sources | string |
Input/Output Ports
The element has 1 input port:
Name in GUI: Input sequences
Name in Workflow File: in-sequence
Slots:
| Slot In GUI | Slot in Workflow File | Type |
|---|---|---|
| Sequence | sequence | string |
The element has 1 output port:
Name in GUI: DAS annotations
Name in Workflow File: out-annotations
Slots:
| Slot In GUI | Slot in Workflow File | Type |
|---|---|---|
| Set of annotations | annotations | annotation-table-list |