In this tutorial, we will show you how amino acid (AA) sequences are registered in the Amino Acid database.
1. Register AA sequences
You can register DNA sequences directly via upload of AA sequence files or indirectly via upload of DNA sequence files. Each time an AA sequence record is created, a protein material associated with the AA sequence is created and registered in the ‘Protein Materials’ library.
1.1. Direct method: From the header, go to ‘Materials’ > ‘Amino Acid Sequences’. This will take you to the ‘Amino Acid Sequences’ library, which lists all unique AA sequences registered in the app.
1.1a. To create a new AA sequence manually or upload sequence files in bulk, click on ‘Upload’ and select ‘Amino Acid Sequences’. This opens the ‘Upload Sequences’ dialog in which you can choose to either paste the sequence or upload sequence files. Click ‘Paste Sequence’ to manually create an AA sequence. Give the sequence a name (naming is optional but highly recommended), type or paste the sequence into the ‘Sequence’ field. Click ‘Submit’ to register the sequence to the ‘Amino Acid Sequences’ library. This also automatically creates a protein material record of this sequence in the ‘Protein Materials’ library.
1.1b. To upload AA sequences in bulk, you can either zip all the files (currently supported Genpept and FASTA files) into a compressed folder or multi-select the individual sequence files and drop the zip folder or the files to the ‘Upload Sequences’ and click ‘Submit’. This will register the sequences in these files to the ‘Amino Acid Sequences’ library and creates a corresponding protein material record in the ‘Protein Materials’ library. If you want to tag the sequences being uploaded/created with specific labels, click ‘Add Tag’ to select pre-made tags or create a new tag.
1.2 Indirect method: AA sequence records can also be created automatically when a DNA sequence is uploaded if the DNA sequence contains coding sequences (CDS). The CDS sequences are translated into the AA sequences and these translated sequences are registered as AA sequences in the ‘Amino Acid Sequences’ library.
2. Amino acid sequence attributes in AA Sequences library view
Figure 1: View of Amino Acid Sequences library
Name: Name of the AA sequence, usually the name of the sequence in the uploaded sequence files
Extinction Coefficient: a number represents how much lights the protein absorbs at a certain wave length. (See More)
Histidine Tag: the location of the his-tag in the AA sequence (Eg. N-term, C-term)
Isoelectric Point: the pH at which the AA sequence has no net charge.
Molecular Weight: the molecular weight (in gram per mol) of the AA sequence.
UnitProt ID: reference ID of the AA sequence (protein) in UnitProt Database
Sequence Length: the length of the AA sequence (the number of amino acids).
Sequence: the AA sequence
Tags: list of all the tags applied to the sequence (defined by users)
Lab Group: the lab group in which the sequence data is belong to (defined by users)
Created By, Created, Modified: the user who creates the sequence, the time it was created and modified, respectively.
3. Delete, view and update AA sequences
3.1 Delete: Multiple sequences can be deleted simultaneously by selecting sequences, right-click and select ‘Delete’.
3.2 View and Update: When double-clicking on a sequence, you are directed to the sequence record view in which sequence information is shown together with options to update or delete the sequence. In this record view, the protein coding sequences are the CDS sequences from which the AA sequence is translated. Currently, you can only update the sequence’s tags and extended properties.