CAS Registry BLAST logo

Search by Sequence or Sequence Identifier

Requirement: Microsoft Windows® XP or higher.

Find subject sequences that are similar to your nucleotide or protein sequence by entering a:

Before You Begin

To search for similar nucleotide or protein sequences:

  1. Access the Result Set Manager in CAS Registry BLAST.

  2. Access your search type:

    To search by:

    Use either of these methods:


    From the Toolbar

    From the menu bar


    Sequence toolbar button Click the Sequence icon.
    The Search by Sequence window displays.
    Select Search > Similar Sequences.
    The Search by Sequence window displays.

    Sequence Identifier

    Sequence ID toolbar button Click the Sequence ID icon.
    The Similar Sequence using Sequence Identifier window displays.
    Select Search > Similar Sequences using Sequence Identifier.
    The Similar Sequence using Sequence Identifier window displays.
  3. (Optional) Enter a Result Name. Otherwise, a default name will be assigned.

    Default name format: Result - nnnnnn

  4. Enter your query.

    Size restriction: All queries are restricted to 50,000 characters.

    For this Explore type:

    Follow these guidelines:


    Enter your sequence in the appropriate format (FASTA, bare sequence, GCG) and follow these guidelines:

    • Type your query, paste, select Read from file..., or click Recall Sequence.
    • Data read from file – Data read from a file overwrites anything previously entered in the query input box.
    • No multiple queries – Multiple queries are not accepted.
    • Blank lines – Blank lines are ignored. (This will cause multiple queries separated by blank lines to be erroneously read as a single query.)
    • Cancel – Selecting Cancel at any time exits sequence searching and returns you to the Result Set Manager window.

    Sequence Identifier

    Type or paste a single number in a supported format:

    • Registry Number —  Any single-sequence CAS Registry Number

      Restriction: "Multichain"  records are not supported.

    • GenBank Accession Numbers —  For nucleic acid or protein records.

      Case: Letters may be entered in upper or lower case.

      Restrictions: GenBank Accession Numbers for CONTIG records are not supported.
      Accession numbers are translated into the corresponding Registry Number before searching. If a Registry Number cannot be retrieved, you will receive a message.

  5. Select the BLAST program for your query.

    The available protein or nucleotide database subset choices display, as appropriate.

  6. Accept the default (all available subsets) or choose which database subsets to search.

  7. If desired, choose Only retrieve sequences with 50 residues or less.

    When to use: When you have a short query sequence and want to ensure that you see the shorter answers (subject sequences) that are returned.

    Short queries can match both long and short sequences, producing many answers. This ensures that matches are limited to short sequences.

    E value: If you select this option, adjust your E value as discussed in Searching Short Sequences.

    Restrictions: This option is NOT available:


  8. Click OK.

    The Settings window for your program displays.

  9. Accept the Basic Options defaults.
    – or –
    Choose new values (as appropriate) for the basic options that apply to your program.

  10. Select Show Additional Options to adjust the additional options as appropriate, or accept the default values.

  11. Click OK to submit your search.

    When a search is submitted, CAS Registry BLAST:

  12. From the Result Set Manager, you can perform these and other functions:

    You can also manipulate your results or the appearance of the listing in the Result Set Manager:


See also

Reports Tab (Result Set Manager)

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.

Unless designated otherwise, all other information Copyright © 1997-2017 by the American Chemical Society. All rights reserved.