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Home   •   Support and Training  •  SciFinder  •  How To Guides  •  Explore by Sequence
How to... Explore by Sequence
  

Explore by Nucleotide or Protein Sequence uses the BLAST search technology to find similar sequences and link to relevant patents and journal articles.


1. Choose an Explore by Sequence option. For example, click Similar Sequences.

blast 1 image 

Tips

  • Pick the option that best meets your needs:
    If you know the... Click...
    Sequence itself Similar Sequences
    CAS Registry Number or GenBank Number

    Similar Sequences using Sequence Identifier

 

 

 

  • Use the Results Set Manager to view previous BLAST results, rename and delete results, set up and review Keep Me Posted results.

Note: Fast BLAST is only available if you have already conducted an Explore by Sequence task within the same session.


2.

Name your result set. Then copy/paste the sequence into the entry box, or click Read from File to import the sequence from a file. Click OK.

blast 2 image

Tips

  • Use the sequence input formula that you have. SciFinder accepts standard GCG, FASTA, ASCII text, and SciFinder formats. Numbers, spaces, and other data are ignored.
  • The Recall Sequence button is active if you have already conducted a sequence search during your session. Use this option to recall a previously searched sequence and quickly start multiple searches using alternate BLAST programs or requirements.

3.

Specify how you would like SciFinder to explore your sequence.  Select a BLAST algorithm. For example, click BLASTp.

blast 3 image 

Select databases or subsets to include in your search.

blast 4 image 

Tips

  • Select "Referenced in at least one patent document" to only retrieve sequences cited in at least one patent.

    Note: A particular sequence may also be cited in other types of documents, in addition to the patent. Therefore, if you later Get References for a sequence (or group of sequences), you will likely retrieve multiple types of documents.
  • Select "Only retrieve sequences with 50 residues or less" when you are searching short sequences and desire similar length answers. This ensures that SciFinder excludes long sequences, which have a high probability of including your short query sequence.
Choose search parameters. You can set the maximum from 1 to 1000 answers. Click OK.

blast 5 image

Tips

  • Select Show Additional Options to view SciFinder's default BLAST settings.

    Note: The default settings are useful for most BLAST searches. However, you may wish to adjust the settings if you are familiar with BLAST searching options. See the SciFinder Help files for information about each of the settings.

3. In the Result Set Manager, the Status column indicates when the search is complete. Select the result and click View Results.

blast 6 image 

Tips

  • Click a column heading to sort results based on that column. Click the column heading again to reverse the order.

    Note: The current sort field and direction are denoted by the arrow in the column heading.
  • To reorder columns, click and drag a column heading to a new location.
  • Right-click on a result to see available options.

3.

Use the Sequence Explore Result to explore your result set. As you explore, select sequences of interest. Click Get References to retrieve corresponding articles and patents.

blast 7 image 

Tips

    Click...

    To ...

    An Alignment Score button

    Select the sequences within that score range.

    Note: Check boxes for those sequences become selected within the Alignment Details area.

    An Alignment Summary bar

    Jump to the corresponding sequence within the Alignment Details list.

    Note: Hovering over a bar displays the sequence name.

    A "+" button

    View Alignment Details for the sequence, e.g., length, score, alignment between the query and result sequences.

    A "box" button

    View redundant sequences for the grouping.

    A Name/CAS Registry Number link

    View substance details for the sequence.

    Check boxes

    Select sequences for further use.

For example, click the + and the box to see redundant sequences and other alignment details.

blast 8 image 

3. Specify the type of references you would like to retrieve. Click OK.

blast 10 image 

Tips

  • Select the check box near the bottom if you are interested in retrieving references that identify the sequence structures as well as studies that discuss activity, disease, and other relationships.

3. Review the references that discuss the sequences. To view details for a particular reference, click the corresponding microscope button.

blast 11 image

blast 12 image

Updated: 5/27/2009 2:41:07 PM
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