seqviewer

Visualize and interactively explore biological sequences

Syntax

seqviewer

seqviewer(Seq)

seqviewer(Seq,Name,Value)

seqviewer('close')

Description

seqviewer opens the Sequence Viewer app.

seqviewer(Seq) loads a sequence Seq into the app, where you can view and interactively explore the sequence.

seqviewer(Seq,Name,Value) opens the app with additional options specified by one or more Name,Value pair arguments.

seqviewer('close') closes the Sequence Viewer app.

Input Arguments

Seq — Amino acid or nucleotide sequence

character vector | string | row vector of integers | structure

Amino acid or nucleotide sequence, specified as:

• Character vector or string containing single-letter codes or a file name with an extension of .gbk, .gpt, .fasta, .fa, or .ebi.

• Row vector of integers

• MATLAB^® structure containing a Sequence field that contains an amino acid or nucleotide sequence, such as returned by fastaread, fastqread, getgenpept, genpeptread, getpdb, pdbread, emblread, getembl, genbankread, or getgenbank

Name-Value Arguments

Specify optional pairs of arguments as Name1=Value1,...,NameN=ValueN, where Name is the argument name and Value is the corresponding value. Name-value arguments must appear after other arguments, but the order of the pairs does not matter.

Before R2021a, use commas to separate each name and value, and enclose Name in quotes.

Example: 'Alphabet','AA' specifies that the aligned sequences are amino acid sequences.

Alphabet — Type of aligned sequences

'AA' | 'NT'

Type of aligned sequences, specified as 'AA' for amino acid sequences or 'NT' for nucleotide sequences.

Example: 'Alphabet','AA'

Examples

Open and View a Biological Sequence

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')

Version History

Introduced before R2006a