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MATLAB BIOINFORMATICS TOOL
RIDA KHALID
MATLAB INTRODUCTION
• MATLAB is a collection of mathematical and
computational projects.
• A MathWorks Web site, MATLAB Tu...
Bioinformatics Toolbox Product
Description
• It provide an integrated software environment for
genome and proteome analysi...
ADVANTAGES
• Read, analyze, and visualize genomic and proteomic
data
• You can explore and visualize this data with sequen...
GENE SELECTED
FUNCTIONS
• One of the biggest advantages of MATLAB is that it
provides an extensive function library.
• Using these funct...
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 se...
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 ...
SEQSHOWORF
SEQSHOWORF
SEQSHOWORF
4-FUNCTION
NWALIGN
• Globally align two sequences using Needleman-Wunsch
algorithm.
• [Score, Alignment] = nwalign(Seq1,Se...
5-FUNCTION
SWALIGN
• [Score, Alignment] = swalign(Seq1, Seq2)
• SmithWaterman Algo
• [Score, Alignment] = swalign(Seq1, Se...
6-FUNCTION
SEQDOTPLOT
• Create dot plot of two sequences.
• seqdotplot(Seq1,Seq2, Window, Number) plots
sequence matches w...
SEQDOTPLOT
7-FUNCTION
AMINOLOOKUP
• Find amino acid codes, integers, abbreviations,
names, and codons.
aminolookup(SeqAA)
• Convert a...
8-FUNCTION
BASELOOKUP
• baselookup('Complement', SeqNT)
• baselookup('Complement', SeqNT) displays the
complementary nucle...
9-FUNCTION
BASECOUNT
• Count nucleotides in sequence.
• NTStruct = basecount(SeqNT)
• Count the bases in a DNA sequence an...
10-FUNCTION
BASECOUNTGRAPH
• Use the function basecount with the chart option to
visualize the nucleotide distribution.
• ...
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(S...
15-FUNCTION
CODONCOUNT
• Codons = codoncount(SeqNT)
• Codons = codoncount(SeqNT) counts the codons in SeqNT, a
nucleotide ...
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)
Matlab bioinformatics presentation
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Matlab bioinformatics presentation

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Matlab bioinformatics presentation

  1. 1. MATLAB BIOINFORMATICS TOOL RIDA KHALID
  2. 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. 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. 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. 5. GENE SELECTED
  6. 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. 7. 1-FUNCTION GETGENBANK • Retrieve sequence information from GenBank database. • Data = getgenbank(AccessionNumber)
  8. 8. GETGENBANK
  9. 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. 10. SEQTOOL
  11. 11. SEQTOOL
  12. 12. SEQTOOL
  13. 13. SEQTOOL
  14. 14. SEQTOOL
  15. 15. SEQTOOL
  16. 16. SEQTOOL
  17. 17. SEQTOOL
  18. 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. 19. SEQSHOWORF
  20. 20. SEQSHOWORF
  21. 21. SEQSHOWORF
  22. 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. 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. 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. 25. SEQDOTPLOT
  26. 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. 27. 8-FUNCTION BASELOOKUP • baselookup('Complement', SeqNT) • baselookup('Complement', SeqNT) displays the complementary nucleotide sequence. • Convert a nucleotide sequence to its complementary sequence.
  28. 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. 29. 10-FUNCTION BASECOUNTGRAPH • Use the function basecount with the chart option to visualize the nucleotide distribution. • basecount(humanHEXA,'chart','pie');
  30. 30. 11-FUNCTION DNA2RNA • Convert DNA sequence to RNA sequence. • SeqRNA = dna2rna(SeqDNA)
  31. 31. 12-FUNCTION RNA2DNA • Convert RNA sequence to DNA sequence • rna2dna(SeqRNA)
  32. 32. 13-FUNCTION NT2AA • Convert nucleotide sequence to amino acid sequence. • nt2aa(SeqNT)
  33. 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. 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. 35. CODONCOUNT
  36. 36. 16-FUNCTION SEQWORDCOUNT • Count number of occurrences of word in sequence. • seqwordcount(Seq, Word)
  37. 37. 17-FUNCTION JOINEDSEQ • Join two sequences to produce supersequence. • SeqNT3 = joinseq(SeqNT1, SeqNT2)

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