January 20, 2021

Biosequence Searching (BLAST)

Basic Local Alignment Search Tool (BLAST) is accessible on the home page by selecting the Biosequences search option. Biosequence searching is not included in the All search and is only available on the home page.

Selecting the Biosequences search option presents the user with the BLAST search interface. The user has the option to manually enter or paste sequence text in the search box or can upload a text or FASTA file by clicking the Upload Sequence button. Up to one hundred sequences can be searched if entered in FASTA format. The user has the option to choose the sequence type they are searching, the domain (nucleotides or proteins) they are searching within, as well as the limit of search results they would like to be displayed. There is also an option for an Advanced Biosequence Search.

Clicking the Advanced Biosequence Search option displays the BLAST search options available with the default setting selected. The options and defaults are dynamically updated depending on the type of sequence and the domain they are searching within.

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

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

If multiple sequences were searched, the count of sequences displays in the search history and the option to view the individual sequences is available. The results of the sequence search can be viewed independently or as a group and completed sequence search results can be viewed before all the sequence searches of a batch search request are complete.

Selecting a View Results button from the search history displays the search results. A summary of the search details displays along with filters for E-Value, Query Coverage %, Subject Coverage %, and Sequence Identity %.

  

If multiple sequences were searched and displayed, an option to view the results of each search displays. However, only the results for one sequence search can be viewed at a time.

For each sequence result, an alignment visualization displays that corresponds with the alignment details contained 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 tabs for the Subject and References. The Subject tab displays the sequence code, the length of the sequence, and the complete sequence in a tabular format.

The Reference tab displays the patents in which the sequences were published. Clicking the References button opens a new tab containing all of the basic patents displayed in the References tab.

See Find Biosequences.

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Bioscape Analysis

Bioscape is a biosequence search-related feature that allows the user to visualize the similarity and patent landscape for a set of sequence results. A Create Bioscape Analysis button is present in the result set above the filters.

Clicking the Create Bioscape Analysis button launches Bioscape in a new tab. The location of the sequence in the visualization corresponds to the similarity of the sequence to the query and the height of the sequence in the visualization corresponds to the number of patents in which the sequence has been published.

See Bioscape Analysis.

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Chemscape Analysis

Chemscape visualizes the similarity and patent landscape for a set of substance results. When viewing a substance result set that is based on a structure search, an option to Create Chemscape Analysis displays.

Clicking Create Chemscape Analysis launches Chemscape in a new tab. The location of the substance in the visualization corresponds to the similarity of the substance to the query and the height of the substance in the visualization corresponds to the number of patents in which the substance has been published.

See Chemscape Analysis.

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