March 2, 2021

Biosequence Searching – CDR

Complementarity-determining regions (CDR) biosequence searching is accessible on the home page by clicking the Biosequences search type.

The CDR search interface is accessed by clicking the CDR tab.

The user has the option to manually enter or paste sequence text in the search boxes or can upload a text or FASTA file by clicking the Upload Sequence button. If more than three CDRs are contained in the text of FASTA file, only the first three will be imported and the user will be notified.

There is not an Advanced Biosequence Search option when CDR is selected.

Once one or more CDRs have been entered in the search boxes, the Start Biosequence Search button will become enabled. After clicking the Start Biosequence Search button, the user will be notified that the search has been submitted.

The status of the search is available in the search history; when the search is complete, a View Results button becomes available.

Clicking the View Results button in the search history displays the search results. The query details and a Venn diagram are provided along with filters for E-Value, Query Coverage %, Subject Coverage %, and Alignment Identity %.

The Venn diagram visualizes the segments present in the result set. Users may view individual or intersecting CDR segment results by selecting the segment and clicking the Apply button.

Once a segment filter is applied, a Reset Segments option becomes enabled; clicking the option resets the biosequence result set to include all results.

For each sequence result present in the result set, there is an alignment visualization that corresponds to the details displayed in the Alignment tab below. Mismatches are highlighted in red in both the visualization and the Alignment tab.

In addition to the Alignment tab, there are also Subject and References tabs. The Subject tab displays the sequence code, the length of the sequence, and the complete sequence in a tabular format.

The References tab displays the patents in which the sequence was published along with the assignee, patent number, and Seq ID number. Clicking the References button opens a reference result set of all the patents included in CAplus.

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Biosequence Searching – Motif

Motif biosequence searching is accessible on the home page by clicking the Biosequences search type.

The Motif search interface is accessed by clicking the Motif tab. The user must manually enter or paste sequence text in the search box as there is no option to upload a text or FASTA file. The user has the option to choose the sequence type they are searching (nucleotide or protein). There is also an Advanced Biosequence Search option.

Clicking the Advanced Biosequence Search option displays the Motif search options available with the default settings selected.

Once a query sequence is entered in the search box, the Start Biosequence Search button becomes enabled. After clicking the Start Biosequence Search button, the user is notified the search was submitted.

The status of the search is available in the search history; when the search is complete, a View Results button becomes available.

If the Motif search query contains variables, the query is enumerated into the various sequences represented by the query string. The user can view all of the results or the results for any one of the completed enumerated queries.

Clicking a View Results button in the search history displays the search results. The Motif search details are provided along with filters for E-Value, Query Coverage %, Subject Coverage %, and Alignment Identity %.

If viewing the results for more than one Motif sequence, a menu is present to view all query search strings. The results for sequence 1 are displayed by default.

To view the results of a different sequence, click the sequence text.

For each sequence result present in the result set, there is an alignment visualization that corresponds to the details displayed in the Alignment tab below. Mismatches are highlighted in red in both the visualization and the Alignment tab.

In addition to the Alignment tab, there are also Subject and References tabs. The Subject tab displays the sequence code, the length of the sequence, and the complete sequence in a tabular format.

The References tab displays the patents in which the sequence was published along with the assignee, patent number, and Seq ID number. Clicking the References button opens a reference result set of all the patents included in CAplus.

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Bioscape for CDR and Motif

Bioscape is also available for CDR and Motif biosequence search results, and the operation and capabilities are the same as for BLAST searching.

See Bioscape Analysis.

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Download BLAST Biosequence Results in .xlsx Format

Download of BLAST search results is now enabled. Clicking the Download icon downloads the result set (up to 100 biosequences) in Excel (.xlsx) format. The Excel spreadsheet contains the following columns:

A – Alignment Image

B – Alignment Text

C – Sequence Length

D – CAS Registry Number (if applicable)

E – Number of Patents

F – Patent No.

G – Sequence ID

H – E-Value

I – BLAST Score

J – Matches

K – Mismatches

L – Alignment Identity

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