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seqdisp

Format long sequence output for easy viewing

Syntax

seqdisp(Seq)
seqdisp(Seq,……”Row',RowValue,……)
seqdisp(Seq,……”Column',ColumnValue,……)
seqdisp(Seq,……”ShowNumbers',ShowNumbersValue,……)

Arguments

Seq

Nucleotide or amino acid sequence represented by any of the following:

  • Character array

  • String vector

  • Character vector containing the FASTA file name

  • MATLAB®structure with the fieldSequence

Multiply aligned sequences are allowed.

FASTA files can have the file extensionfa,fasta,fas,fsa, orfst.
RowValue 整数,指定的长度each row. Default is60.
ColumnValue Integer that specifies the column width or number of symbols before displaying a space. Default is10.
ShowNumbersValue Controls the display of numbers at the start of each row. Choices aretrue(default) to show numbers, orfalseto hide numbers.

Description

seqdisp(Seq)displays a sequence in rows, with a default row length of 60 and a default column width of10.

seqdisp(Seq,……”PropertyName',PropertyValue,……)callsseqdispwith optional properties that use property name/property value pairs. You can specify one or more properties in any order. EachPropertyNamemust be enclosed in single quotation marks and is case insensitive. These property name/property value pairs are as follows:

seqdisp(Seq,……”Row',RowValue,……)specifies the length of each row for the displayed sequence.

seqdisp(Seq,……”Column',ColumnValue,……)specifies the number of letters to display before adding a space.RowValuemust be larger than and evenly divisible byColumnValue.

seqdisp(Seq,……”ShowNumbers',ShowNumbersValue,……)controls the display of numbers at the start of each row. Choices aretrue(default) to show numbers, orfalseto hide numbers.

Examples

Read sequence information from the GenBank®database. Display the sequence in rows with 50 letters, and within a row, separate every 10 letters with a space.

mouseHEXA = getgenbank('AK080777'); seqdisp(mouseHEXA, 'Row', 50, 'Column', 10)

Create and save a FASTA file with two sequences, and then display it.

hdr = ['Sequence A'; 'Sequence B']; seq = ['TAGCTGRCCAAGGCCAAGCGAGCTTN';'ATCGACYGGTTCCGGTTCGCTCGAAN'] fastawrite('local.fa', hdr, seq); seqdisp('local.fa', 'ShowNumbers', false') ans = >Sequence A 1 TAGCTGRCCA AGGCCAAGCG AGCTTN >Sequence B 1 ATCGACYGGT TCCGGTTCGC TCGAAN

See Also

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Introduced before R2006a

Bioinformatics Toolbox Documentation

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