• MATLAB is a collection of mathematical and
• A MathWorks Web site, MATLAB Tutorials and
Learning Resources, offers a number of introductory
videos and a PDF manual entitled Getting Started
• MATLAB (matrix laboratory) is a multi-paradigm
numerical computing environment and fourth-
generation programming language.
Bioinformatics Toolbox Product
• It provide an integrated software environment for
genome and proteome analysis.
• It helps in building applications for drug discovery
and design, genetic engineering, and biological
• Read, analyze, and visualize genomic and proteomic
• You can explore and visualize this data with sequence
browsers, phylogenetic tree, and clustergrams.
• Sequence analysis, visualization including pairwise,
multiple sequence alignment and peak detection is
• You can read genomic and proteomic data from
standard file formats such as SAM, FASTA, CEL, and
CDF, as well as from online databases such as the
NCBI, Gene Expression, Omnibus and GenBank.
• One of the biggest advantages of MATLAB is that it
provides an extensive function library.
• Using these functions is an important part of writing
functional and efficient MATLAB code.
• Command window
• Retrieve sequence information from GenBank
• Data = getgenbank(AccessionNumber)
• Open Sequence Tool window to interactively
explore biological sequences.
• Retrieve a sequence from the GenBank database.
S = getgenbank('NM_000520');
• Load the sequence into the Sequence Tool
• Display open reading frames in sequence
• Locate open reading frames (ORFs) in the human
gene. For example, for the human gene HEXA, type
humanORFs = seqshoworfs(humanHEXA.Sequence)
• Globally align two sequences using Needleman-Wunsch
• [Score, Alignment] = nwalign(Seq1,Seq2) returns N character
array showing the two sequences, Seq1 and Seq2and shows
• [Score, Alignment] = swalign(Seq1, Seq2)
• SmithWaterman Algo
• [Score, Alignment] = swalign(Seq1, Seq2) returns N-character
array showing the two sequences, Seq1 and Seq2 and shows
• Create dot plot of two sequences.
• seqdotplot(Seq1,Seq2, Window, Number) plots
sequence matches when there are at least Number
matches in a window of size Window.
• Calculate reverse strand of nucleotide sequence.
• SeqR = seqreverse(SeqNT)
• SeqR = seqreverse(SeqNT) calculates the reverse
strand of a DNA or RNA nucleotide sequence. The
return sequence, SeqR, reads from 3' --> 5' and is in
the same format as SeqNT.
• Codons = codoncount(SeqNT)
• Codons = codoncount(SeqNT) counts the codons in SeqNT, a
nucleotide sequence, and returns the codon counts in
Codons, a MATLAB structure containing fields for the 64
possible codons (AAA, AAC, AAG, ..., TTG, TTT).