Sequence Viewer

Visualize and interactively explore biological sequences

Description

The Sequence Viewer app lets you visualize and explore amino acid or nucleotide sequences.

You can:

Import sequences from the NCBI or EMBL databases directly.
View and explore various sequence information (such as ORFs and CDSs) and basic statistics (such as percentages of base counts or amino acid counts).
View the complement and reverse complement sequences, and other sequence features such as genes and exons.
Extract protein coding sections of a nucleotide sequence and export them to the MATLAB^® workspace.
Search for characteristic words or sequence patterns using regular expressions.

MATLAB Toolstrip: On the Apps tab, under Computational Biology, click the app icon.
MATLAB command prompt: Enter seqviewer.

Retrieve a sequence from the GenBank^® database.

S = getgenbank('M10051');

Load the sequence into the Sequence Viewer app.

seqviewer(S)

Alternatively, you can click Sequence Viewer on the Apps tab to open the app, and view the biological sequence S.

Close the app.

seqviewer('close')

seqviewer opens the Sequence Viewer app.

seqviewer(Seq) loads a amino acid or nucleotide sequence Seq into the app. Seq can be one of the following:

A string of single-letter codes
A row vector of integers
A MATLAB structure containing a Sequence field that contains an amino acid or nucleotide sequence, such as the structure returned by fastaread, fastqread, getgenpept, genpeptread, getpdb, pdbread, emblread, getembl, genbankread, or getgenbank
A string specifying a file name with an extension of .gbk, .gpt, .fasta, .fa, or .ebi.