General Template databases can be used with our Peptide Annotator, which is used to annotate and cluster protein and peptide sequences. If you are unsure what a reference database is, see Understanding Reference Databases.
Jump to:
What kinds of sequences can I use?
A General Template database can be used for analyzing the sequencing data from any biological molecule. This is different from our Germline Gene and Antibody Template databases, which are specific to antibody/TCR sequences.
Your reference sequences might include:
- Peptides
- Proteins
- Protein domains - for example CDR3s
Note: we do not currently support non-standard amino acids
Key requirements for reference sequence(s):
- Ensure that your reference sequences are trimmed to the actual region of interest
- The matching and clustering will be performed on the full length of sequence you upload as a reference, regions within the reference sequence will not automatically be pulled out and clustered upon.
- Either amino acid or nucleotide sequence(s) can be used
- Multiple sequences can be part of the reference database, for easier management these can be in a Sequence List (see Grouping Sequences)
- The reference sequences can be with or without sequence annotations
- Any annotations on the reference database sequences will be carried forward and annotated on your submitted query sequences, if a match to the reference is found.
Each query sequence will be matched to one reference database sequence - we do not yet support identifying different combinations of protein domains on one read. Please let us know if you are interested in this sort of functionality.
Creating a General Template database
Step 1
- First, ensure that your reference sequences are trimmed to the actual region of interest. The matching and clustering will be performed on the full length of sequence you upload as a reference, regions within the reference sequence will not automatically be pulled out and clustered upon.
- Note: Any extra annotations on the reference sequences can however be added. These will be pulled across and annotated on your query sequences.
Step 2
- The Reference Database section can be found on the navigation panel under Organization Databases. To create a new reference database, click on the 3 vertical dots to bring up the New database option:
- Select the General Template database option, and then either choose to upload the sequences upon creation or add sequences to the reference database following its creation.