Getting the Most Out of SciFinder-n: Sequence Searching

Find Sequences - BLAST

To find sequences with BLAST, enter or copy and paste a nucleotide or protein string, or upload a sequence file as a .txt file or .fasta for multiple sequences. Up to 100 sequences can be entered. Then, select the appropriate sequence type for your query, and select the relevant Search Within options. Click Start Sequence Search to begin the search.

On the home page, you can view the results of the search once it is complete. Note that sequence results will expire 30 days after they are first generated. For more information, check out this training video or this help page.

Advanced Searching - BLAST

You can search sequences using parameters like sequence identity percentage, gap costs, and BLAST algorithms. For more information on advanced searching, see this training video or this help page.

Find Sequences - CDR

To search with CDR, enter, copy and paste, or upload up to three CDRs. CDR queries can be a protein string, .txt or .fasta file. Select whether or not to include National Center for Biotechnology Information (NCBI) sequences, and click on the magnifying glass to start the search.

On the home page, you can view the results of the search once it is complete. Note that sequence results will expire 30 days after they are first generated. For more information, check out this training video or this help page.

Find Sequences - Motif

Copy and paste or enter a protein or nucleotide strings. The allowable motif patterns, including regex syntax, and amino acid and nucleotide codes, are listed here. Select the the appropriate sequence type, nucleotide or protein, and check whether to include NCBI (National Center for Biotechnology Information) database entries.

In the advanced sequence search, the default Query Coverage % and E-Value selections may be changed. In addition, Combine Motif Results can be selected to return one set of results across all variants. Click on the Start Sequence Search to begin the search.

On the home page, you can view the results of the search once it is complete. Note that sequence results will expire 30 days after they are first generated. For more information, check out this training video or this help page.

According to CAS, Bioscape Analysis "visualizes the similarity and patent landscape for a set of sequence results. The location of the sequence bar in the visualization corresponds to the similarity of the sequence to the query, and the height of the sequence bar corresponds to the number of patents in which the sequence has been published."

For more information and examples, see these CAS help guides on the following topics:

Change View

Refine Results

Select Multiple Sequence Results