1. MATLAB BIOINFORMATICS TOOL
RIDA KHALID

2. MATLAB INTRODUCTION
• MATLAB is a collection of mathematical and
computational projects.
• A MathWorks Web site, MATLAB Tutorials and
Learning Resources, offers a number of introductory
videos and a PDF manual entitled Getting Started
with MATLAB.
• MATLAB (matrix laboratory) is a multi-paradigm
numerical computing environment and fourth-
generation programming language.

3. Bioinformatics Toolbox Product
Description
• 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
research.

4. ADVANTAGES
• Read, analyze, and visualize genomic and proteomic
data
• 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
done.
• 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.

5. GENE SELECTED

6. FUNCTIONS
• 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

7. 1-FUNCTION
GETGENBANK
• Retrieve sequence information from GenBank
database.
• Data = getgenbank(AccessionNumber)

8. GETGENBANK

9. 2-FUNCTION
SEQTOOL
• Open Sequence Tool window to interactively
explore biological sequences.
seqtool(Seq)
• Retrieve a sequence from the GenBank database.
S = getgenbank('NM_000520');
• Load the sequence into the Sequence Tool
window.
seqtool(S)

10. SEQTOOL

11. SEQTOOL

12. SEQTOOL

13. SEQTOOL

14. SEQTOOL

15. SEQTOOL

16. SEQTOOL

17. SEQTOOL

18. 3-FUNCTION
SEQSHOWORF
• Display open reading frames in sequence
seqshoworfs(SeqNT)
• Locate open reading frames (ORFs) in the human
gene. For example, for the human gene HEXA, type
humanORFs = seqshoworfs(humanHEXA.Sequence)

19. SEQSHOWORF

20. SEQSHOWORF

21. SEQSHOWORF

22. 4-FUNCTION
NWALIGN
• Globally align two sequences using Needleman-Wunsch
algorithm.
• [Score, Alignment] = nwalign(Seq1,Seq2) returns N character
array showing the two sequences, Seq1 and Seq2and shows
global alignment.

23. 5-FUNCTION
SWALIGN
• [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
local alignment.

24. 6-FUNCTION
SEQDOTPLOT
• 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.

25. SEQDOTPLOT

26. 7-FUNCTION
AMINOLOOKUP
• Find amino acid codes, integers, abbreviations,
names, and codons.
aminolookup(SeqAA)
• Convert an amino acid sequence in single-letter
codes to the corresponding three-letter
abbreviations.

27. 8-FUNCTION
BASELOOKUP
• baselookup('Complement', SeqNT)
• baselookup('Complement', SeqNT) displays the
complementary nucleotide sequence.
• Convert a nucleotide sequence to its complementary
sequence.

28. 9-FUNCTION
BASECOUNT
• Count nucleotides in sequence.
• NTStruct = basecount(SeqNT)
• Count the bases in a DNA sequence and
return the results in a structure.

29. 10-FUNCTION
BASECOUNTGRAPH
• Use the function basecount with the chart option to
visualize the nucleotide distribution.
• basecount(humanHEXA,'chart','pie');

30. 11-FUNCTION
DNA2RNA
• Convert DNA sequence to RNA sequence.
• SeqRNA = dna2rna(SeqDNA)

31. 12-FUNCTION
RNA2DNA
• Convert RNA sequence to DNA sequence
• rna2dna(SeqRNA)

32. 13-FUNCTION
NT2AA
• Convert nucleotide sequence to amino acid
sequence.
• nt2aa(SeqNT)

33. 14-FUNCTION
SEQREVERSE
• 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.

34. 15-FUNCTION
CODONCOUNT
• 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).

35. CODONCOUNT

36. 16-FUNCTION
SEQWORDCOUNT
• Count number of occurrences of word in sequence.
• seqwordcount(Seq, Word)

37. 17-FUNCTION
JOINEDSEQ
• Join two sequences to produce supersequence.
• SeqNT3 = joinseq(SeqNT1, SeqNT2)