MATLAB BIOINFORMATICS TOOLRIDA KHALID

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.

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.

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.

GENE SELECTED

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

1-FUNCTION GETGENBANK

• Retrieve sequence information from GenBank database.

• Data = getgenbank(AccessionNumber)

GETGENBANK

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)

SEQTOOL

SEQTOOL

SEQTOOL

SEQTOOL

SEQTOOL

SEQTOOL

SEQTOOL

SEQTOOL

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, typehumanORFs = seqshoworfs(humanHEXA.Sequence)

SEQSHOWORF

SEQSHOWORF

SEQSHOWORF

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.

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.

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.

SEQDOTPLOT

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.

8-FUNCTION BASELOOKUP

• baselookup('Complement', SeqNT)• baselookup('Complement', SeqNT) displays the

complementary nucleotide sequence.• Convert a nucleotide sequence to its complementary

sequence.

9-FUNCTION BASECOUNT

• Count nucleotides in sequence.• NTStruct = basecount(SeqNT)• Count the bases in a DNA sequence and return

the results in a structure.

10-FUNCTION BASECOUNTGRAPH

• Use the function basecount with the chart option to visualize the nucleotide distribution.

• basecount(humanHEXA,'chart','pie');

11-FUNCTION DNA2RNA

• Convert DNA sequence to RNA sequence.• SeqRNA = dna2rna(SeqDNA)

12-FUNCTION RNA2DNA

• Convert RNA sequence to DNA sequence• rna2dna(SeqRNA)

13-FUNCTION NT2AA

• Convert nucleotide sequence to amino acid sequence.

• nt2aa(SeqNT)

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.

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).

CODONCOUNT

16-FUNCTION SEQWORDCOUNT

• Count number of occurrences of word in sequence.• seqwordcount(Seq, Word)

17-FUNCTION JOINEDSEQ

• Join two sequences to produce supersequence.• SeqNT3 = joinseq(SeqNT1, SeqNT2)