Use CAS Registry BLAST (Basic Local Alignment Search Tool) to find sequences of interest from patent, journal, and GenBank® sources. You can then:

Import CAS Registry Numbers®, and then use STNext tools and command language to locate substance and bibliographic records.
Create BLAST Alignment Reports to review sequence alignment and score matching details, along with bibliographic and substance information.

Note: Confirm with your administrator that you have installation privileges on your machine.

Sequence Search Query Limits

STN has some general command length limits, and also some specific query length limits for Sequence Code Match (SCM) sequence searching and similarity searching. It is important to note that some of them are not the same in CAS REGISTRY and DGENE, USGENE and PCTGEN.

CAS Registry Limits

SCM Sequence Searching in STNext

Limit of 256 characters for a SCM search at the command prompt: SQEP, SQEFP, SQSFP, SQEN, SQSN. Longer sequences get a command interrupted message.
It is possible to perform an SCM search with longer queries in REGISTRY by using concatenation.

CAS Registry BLAST Similarity Searching

Limit of 50,000 characters for all 5 search modes (BLASTn, BLASTx, tBLASTx, BLASTp, and tBLASTn).

Security

CAS recognizes that sequence queries submitted for BLAST searching and search results are valuable intellectual property. To safeguard this information, CAS Registry BLAST uses 128-bit SSL encryption, the standard for financial transactions and other applications requiring a high level of security.

Cost

For price information for CAS Registry BLAST, enter HELP COST at an arrow prompt when you are in the REGISTRY file.

GenBank® is a registered trademark of the U.S. Department of Health and Human Services for the Genetic Sequence Data Bank.

BLAST® is a registered trademark of the National Library of Medicine.

BLAST® reference information provided in whole or in part from the National Center for Biotechnology Information (NCBI), National Library of Medicine, National Institutes of Health.

Importing Sequence Data CAS Registry Numbers into STNext

On the My Files > Scripts page, click the Import Script button.
Click the Browse button.
Select the sequence script file and click the Open button.
Click the Ok button.
The script appears on the Scripts page with a double helix icon denoting it is a sequence script; click the Run button to run the imported script to create L-Numbers that include all of your sequences.

Creating a BLAST Alignment Report

The BLAST Alignment Report displays sequence alignment and score matching details along with bibliographic and substance information.

Creating the report involves two main tasks:

In CAS Registry BLAST, generate and export sequence data.
In STNext, import sequence data and generate report.

Generating and Exporting Sequence and Alignment Data in CAS Registry BLAST

The procedure below uses a nucleotide a CAS Registry BLASTn sequence query.

Launch CAS Registry BLAST. If needed, download CAS Registry BLAST.
In the Result Set Manager window, click the Sequence icon.
In the Similar Sequences window:
1. Enter a result name.
2. Enter the sequence query by copy/paste or reading data from a file, and then click the OK button.
In the Program Selection window, select the BLAST program for your query.
In the BLAST Database Subsets window, accept the default of All Sequences, and then click the OK button.
In the Settings window, accept the Basic Options defaults, or select new values (as appropriate) for the basic options that apply to your program.
Click the OK button to submit your search. When a search is submitted, CAS Registry BLAST:
1. Creates a sequence query (and queues it if necessary).
2. Performs the search, indicating its status in the Result Set Manager. You can submit additional sequences while the searches are running. When the status column indicates Complete, your result is available. Note: Closing the Result Set Manager window during a running search does not affect its status. The search continues to run in the background.
3. Automatically saves your result set in the Result Set Manager. Note: You may keep a maximum of 100 search queries, regardless of the search status.
On the Reports tab, highlight the result set name, and then click View Results to see the results of your search.
In the Report window, click Alignment Score buttons to select groups of sequences to include in the file, and then click the Get STN Data Script button. Note: Higher Alignment Scores will have better alignment and match over the length of the query.
In the Get STN Data Script window, click the Sequence and Reference Records icon.
Save as a script (.scb) file.

Note: In Preferences, you can specify the folder to which files are saved by clicking the Preferences icon in Result Set Manager.

Click Locations > Folders, and then browse to select the desired folders. You may select up to two levels down into a main directory.
In the next Save File As window, click the Save button to create an STNext Saved Sequences (.xss) file in the same location as the saved script file.

Next, you will import the sequence data to STNext and generate the report.

Importing BLAST Sequence Data into STNext and Generating Report

On the My Files > Scripts page, click the Import Script button.
Click the Browse button.
Select the sequence script file that was created in the CAS Registry BLAST Client, and then click the Open button.
Click the Ok button.
The script appears on the Scripts page with a double helix icon denoting it is a sequence script; click the Run button.
In the first Enter User Data window, enter the display format for the Registry file (e.g., IDE), and then click the Ok button.
In the second Enter User Data window, enter BIB hitrn as the display format for CAplus to highlight Registry Numbers, and then click the Ok button.
After the script completes, go to My Files > Transcripts page, click the ellipsis (...) icon for the currently active transcript, and then select Report.
In the Reporting window, select a template and format for the report, select the Include BLAST Alignment Data box, and then click the Next button.

Note: The Patent and Journal template is recommended for alignment and bibliographic data, and the Substance Report template is recommend for alignment and substance details. The Table format is currently not supported for BLAST Alignment data.
In the Import Alignment Data window, click the Browse button.
Select and open the .xss file.
Click the Next button.
Enter the report title in the Document Title field, select/enter any other optional information, and then click the Download button.