User manual MATLAB BIOINFORMATICS TOOLBOX 3

[. . . ] Bioinformatics ToolboxTM 3 User's Guide How to Contact The MathWorks Web Newsgroup www. mathworks. com/contact_TS. html Technical Support www. mathworks. com comp. soft-sys. matlab suggest@mathworks. com bugs@mathworks. com doc@mathworks. com service@mathworks. com info@mathworks. com Product enhancement suggestions Bug reports Documentation error reports Order status, license renewals, passcodes Sales, pricing, and general information 508-647-7000 (Phone) 508-647-7001 (Fax) The MathWorks, Inc. 3 Apple Hill Drive Natick, MA 01760-2098 For contact information about worldwide offices, see the MathWorks Web site. Bioinformatics ToolboxTM User's Guide © COPYRIGHT 2003­2010 by The MathWorks, Inc. The software described in this document is furnished under a license agreement. The software may be used or copied only under the terms of the license agreement. [. . . ] This structure contains the position of the start and stop codons for all open reading frames (ORFs) on each reading frame. humanORFs = 1x3 struct array with fields: Start Stop The Help browser opens displaying the three reading frames with the ORFs colored blue, red, and green. Notice that the longest ORF is in the first reading frame. 2-26 Example: Sequence Alignment 3 Locate open reading frames (ORFs) in the mouse gene. Type: 2-27 2 Sequence Analysis mouseORFs = seqshoworfs(mouseHEXA. Sequence) seqshoworfs creates the structure mouseORFS. mouseORFs = 1x3 struct array with fields: Start Stop The mouse gene shows the longest ORF on the first reading frame. 2-28 Example: Sequence Alignment Comparing Amino Acid Sequences The following procedure illustrates how to use global and local alignment functions to compare two amino acid sequences. You could use alignment functions to look for similarities between two nucleotide sequences, but alignment functions return more biologically meaningful results when you are using amino acid sequences. After you have located the open reading frames on your nucleotide sequences, you can convert the protein coding sections of the nucleotide sequences to their corresponding amino acid sequences, and then you can compare them for similarities. 1 Using the open reading frames identified previously, convert the human and mouse DNA sequences to the amino acid sequences. Because both the human and mouse HEXA genes were in the first reading frames (default), you do not need to indicate which frame. Type humanProtein = nt2aa(humanHEXA. Sequence); mouseProtein = nt2aa(mouseHEXA. Sequence); 2 Draw a dot plot comparing the human and mouse amino acid sequences. Type seqdotplot(mouseProtein, humanProtein, 4, 3) ylabel('Mouse hexosaminidase A (alpha subunit)') xlabel('Human hexosaminidase A (alpha subunit)') Dot plots are one of the easiest ways to look for similarity between sequences. The diagonal line shown below indicates that there may be a good alignment between the two sequences. 2-29 2 Sequence Analysis 3 Globally align the two amino acid sequences, using the Needleman-Wunsch algorithm. Type [GlobalScore, GlobalAlignment] = nwalign(humanProtein, . . . mouseProtein); showalignment(GlobalAlignment) showalignment displays the global alignment of the two sequences in the Help browser. Notice that the calculated identity between the two sequences is 60%. 2-30 Example: Sequence Alignment 2-31 2 Sequence Analysis The alignment is very good between amino acid position 69 and 599, after which the two sequences appear to be unrelated. Notice that there is a stop (*) in the sequence at this point. If you shorten the sequences to include only the amino acids that are in the protein you might get a better alignment. Include the amino acid positions from the first methionine (M) to the first stop (*) that occurs after the first methionine. 4 Trim the sequence from the first start amino acid (usually M) to the first stop (*) and then try alignment again. Find the indices for the stops in the sequences. humanStops = find(humanProtein == '*') humanStops = 41 599 611 713 722 730 mouseStops = find(mouseProtein == '*') mouseStops = 539 557 574 606 Looking at the amino acid sequence for humanProtein, the first M is at position 70, and the first stop after that position is actually the second stop in the sequence (position 599). Looking at the amino acid sequence for mouseProtein, the first M is at position 11, and the first stop after that position is the first stop in the sequence (position 557). 5 Truncate the sequences to include only amino acids in the protein and the stop. humanProteinORF = humanProtein(70:humanStops(2)) humanProteinORF = MTSSRLWFSLLLAAAFAGRATALWPWPQNFQTSDQRYVLYPNNFQFQYDV SSAAQPGCSVLDEAFQRYRDLLFGSGSWPRPYLTGKRHTLEKNVLVVSVV TPGCNQLPTLESVENYTLTINDDQCLLLSETVWGALRGLETFSQLVWKSA EGTFFINKTEIEDFPRFPHRGLLLDTSRHYLPLSSILDTLDVMAYNKLNV 2-32 Example: Sequence Alignment FHWHLVDDPSFPYESFTFPELMRKGSYNPVTHIYTAQDVKEVIEYARLRG IRVLAEFDTPGHTLSWGPGIPGLLTPCYSGSEPSGTFGPVNPSLNNTYEF MSTFFLEVSSVFPDFYLHLGGDEVDFTCWKSNPEIQDFMRKKGFGEDFKQ LESFYIQTLLDIVSSYGKGYVVWQEVFDNKVKIQPDTIIQVWREDIPVNY MKELELVTKAGFRALLSAPWYLNRISYGPDWKDFYIVEPLAFEGTPEQKA LVIGGEACMWGEYVDNTNLVPRLWPRAGAVAERLWSNKLTSDLTFAYERL SHFRCELLRRGVQAQPLNVGFCEQEFEQT* mouseProteinORF = mouseProtein(11:mouseStops(1)) mouseProteinORF = MAGCRLWVSLLLAAALACLATALWPWPQYIQTYHRRYTLYPNNFQFRYHV SSAAQAGCVVLDEAFRRYRNLLFGSGSWPRPSFSNKQQTLGKNILVVSVV TAECNEFPNLESVENYTLTINDDQCLLASETVWGALRGLETFSQLVWKSA EGTFFINKTKIKDFPRFPHRGVLLDTSRHYLPLSSILDTLDVMAYNKFNV FHWHLVDDSSFPYESFTFPELTRKGSFNPVTHIYTAQDVKEVIEYARLRG IRVLAEFDTPGHTLSWGPGAPGLLTPCYSGSHLSGTFGPVNPSLNSTYDF MSTLFLEISSVFPDFYLHLGGDEVDFTCWKSNPNIQAFMKKKGFTDFKQL ESFYIQTLLDIVSDYDKGYVVWQEVFDNKVKVRPDTIIQVWREEMPVEYM LEMQDITRAGFRALLSAPWYLNRVKYGPDWKDMYKVEPLAFHGTPEQKAL VIGGEACMWGEYVDSTNLVPRLWPRAGAVAERLWSSNLTTNIDFAFKRLS HFRCELVRRGIQAQPISVGCCEQEFEQT* 6 Globally align the trimmed amino acid sequences. Type [GlobalScore_trim, GlobalAlignment_trim] = nwalign(humanProteinORF, . . . mouseProteinORF); showalignment(GlobalAlignment_trim) showalignment displays the results for the second global alignment. Notice that the percent identity for the untrimmed sequences is 60% and 84% for trimmed sequences. 2-33 2 Sequence Analysis 7 Another way to truncate an amino acid sequence to only those amino acids in the protein is to first truncate the nucleotide sequence with indices from 2-34 Example: Sequence Alignment the seqshoworfs function. Remember that the ORF for the human HEXA gene and the ORF for the mouse HEXA were both on the first reading frame. humanORFs = seqshoworfs(humanHEXA. Sequence) humanORFs = 1x3 struct array with fields: Start Stop mouseORFs = seqshoworfs(mouseHEXA. Sequence) mouseORFs = 1x3 struct array with fields: Start Stop humanPORF = nt2aa(humanHEXA. Sequence(humanORFs(1). Start(1):. . . humanORFs(1). Stop(1))); mousePORF = nt2aa(mouseHEXA. Sequence(mouseORFs(1). Start(1):. . . [. . . ] Select multiple branch or leaf nodes by Shift-clicking the nodes, or click-dragging to draw a box around nodes. 4-37 4 Phylogenetic Analysis Use the Select submenu to select specific branch and leaf nodes based on different criteria. · Select By Distance -- Displays a slider bar at the top of the window, which you slide to specify a distance threshold. Nodes whose distance from the selected node are below this threshold appear in red. Nodes whose distance from the selected node are above this threshold appear in blue. [. . . ]