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Parameters in GUI
Parameter | Description | Default value |
---|
Annotate as | Name of the result annotations marking found conserved domains. | CDD result |
Database | Currently, CD-Search is offered with the following search databases: - CDD - this is a superset including NCBI-curated domains and data imported from Pfam, SMART, COG, PRK, and TIGRFAM.
- Pfam - a mirror of a recent Pfam-A database of curated seed alignments. Pfam version numbers do change with incremental updates. As with SMART, families describing very short motifs or peptides may be missing from the mirror. An HMM-based search engine is offered on the Pfam site.
- SMART - a mirror of a recent SMART set of domain alignments. Note that some SMART families may be missing from the mirror due to update delays or because they describe very short conserved peptides and/or motifs, which would be difficult to detect using the CD-Search service. You may want to try the HMM-based search service offered on the SMART site. Note also that some SMART domains are not mirrored in CD because they represent “superfamilies” encompassing several individual, but related, domains; the corresponding seed alignments may not be available from the source database in these cases. Note also that SMART version numbers do not change with incremental updates of the source database (and the mirrored CD-Search database).
- TIGRFAM - a mirror of a recent TIGRFAM set of domain alignments. An HMM-based search engine is offered on the TIGRFAM site.
- COG - a mirror of the current COG database of orthologous protein families focusing on prokaryotes. Seed alignments have been generated by an automated process. An alternative search engine, “Cognitor”, which runs protein-BLAST against a database of COG-assigned sequences, is offered on the COG site.
- KOG - a eukaryotic counterpart to the COG database. KOGs are not included in the CDD superset, but are searchable as a separate data set.
| CDD Available values are: - CDD
- Pfam
- TIGRFAM
- COG
- KOG
- Prk
- SMART
|
Database directory | Specifies database directory for local search. | |
Local search | Perform the search on local machine or submit the search to NCBI for remote execution. | True |
Expect value | Modifies the E-value threshold used for filtering results. False positive results should be very rare with the default setting of 0.01, results with E-values in the range of 1 and above should be considered putative false positives. | |
Parameters in Schema Workflow FileType: cd-search
Parameter | Parameter in the GUI | Type |
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result-name | Annotate as | string |
db-name | Database | string |
db-path | Database directory | string |
local-search | Local search | boolean |
e-val | Expect value | numeric |
Input/Output Ports
The element has 1 input port:
Name in GUI: Input sequence
Name in Schema File Workflow File: in-sequence
Slots:
Slot In GUI | Slot in Schema Workflow File | Type |
---|
Sequence | sequence | sequence |
And 1 output port:
Name in GUI: Annotations
Name in Schema File Workflow File: out-annotations
Slots:
Slot In GUI | Slot in Schema Workflow File | Type |
---|
Set of annotations | annotations | annotation-table |