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UK MRC Human Genome Mapping Project Resource Centre http://www.hgmp.mrc.ac.uk EMBOSS – an application suite for bioinformatics Lisa Mullan
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UK MRC Human Genome Mapping Project Resource Centre http://www.hgmp.mrc.ac.uk E – European M – Molecular B – Biology O – Open S – Software S - Suite
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UK MRC Human Genome Mapping Project Resource Centre http://www.hgmp.mrc.ac.uk Large collection of gene and protein analysis tools Sequence retrieval Alignments Primer design Restriction Mapping Protein domain searching Translation
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UK MRC Human Genome Mapping Project Resource Centre http://www.hgmp.mrc.ac.uk DNA Sequence 1 DNA Sequence 2 dotplottranslation protein local/global alignment protein Sequence 1 protein Sequence 2 multiple sequence alignment motif and domain searching physico- chemical properties
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UK MRC Human Genome Mapping Project Resource Centre http://www.hgmp.mrc.ac.uk AGTGGTCGTGAAG AGAATGCTCCTCC TTTGGAATCTTAA >SEQ1.fasta AGTGCTCCTCCCT TAGAATCTTAG >SEQ2.fasta Unix% dottup SEQ1.fasta SEQ2.fasta –window 10 & Unix% dotmatcher SEQ1.fasta SEQ2.fasta –window 10 – threshold 17 & For an exact match: For a similarity match: Dotplots
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UK MRC Human Genome Mapping Project Resource Centre http://www.hgmp.mrc.ac.uk ATGGGTCGTGAAGAGAATGCTCCTCCTTTGGAATCT TCTAAGATTCCCTCCTCGGTATCTAAGATTCCCTCCTCGGTA Dottup looks for regions of exact match Dotplots
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UK MRC Human Genome Mapping Project Resource Centre http://www.hgmp.mrc.ac.uk ATGGGTCGTGAAGAGAATGCTCCTCCTTTGGAATCT TCTAAGATTCCCTCCTCGGTATCTAAGATTCCCTCCTCGGTA Dottup looks for regions of exact match There are no regions of exact match spanning a window size of between the vertical window of 10 and the horizontal sequence, therefore nothing is placed on the output graph. Dotplots
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UK MRC Human Genome Mapping Project Resource Centre http://www.hgmp.mrc.ac.uk ATGGGTCGTGAAGAGAATGCTCCTCCTTTGGAATCT TCTAAGATTCCCTCCTCGGTATCTAAGATTCCCTCCTCGGTA There are no regions of exact match spanning a window size of 10 anywhere between the two sequences, therefore nothing is placed on the output graph. Dotplots
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UK MRC Human Genome Mapping Project Resource Centre http://www.hgmp.mrc.ac.uk A T G C A 5 -4 -4 -4 T -4 5 -4 -4 G –4 -4 5 -4 C -4 -4 -4 5 Identity Matrix Dotplots
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UK MRC Human Genome Mapping Project Resource Centre http://www.hgmp.mrc.ac.uk A T G C A 5 -4 -4 -4 T -4 5 -4 -4 G –4 -4 5 -4 C -4 -4 -4 5 CCTCCTTTGG Score = 50 5555555555 CCTCCTTTGG CCTCCCTTAG 55-455555 5 Score = 32 ProLeu ProLeu Dotplots
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UK MRC Human Genome Mapping Project Resource Centre http://www.hgmp.mrc.ac.uk ATGGGTCGTGAAGAGAATGCTCCTCCTTTGGAATCT TCTAAGATTCCCTCCTCGGTATCTAAGATTCCCTCCTCGGTA Using a window size of 10 and a threshold value of 25 Dotplots
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UK MRC Human Genome Mapping Project Resource Centre http://www.hgmp.mrc.ac.uk ATGGGTCGTGAAGAGAATGCTCCTCCTTTGGAATCT TCTAAGATTCCCTCCTCGGTATCTAAGATTCCCTCCTCGGTA Using a window size of 10 and a threshold value of 35 Dotplots
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UK MRC Human Genome Mapping Project Resource Centre http://www.hgmp.mrc.ac.uk ATGGGTCGTGAAG AGAATGCTCCTCC TTTGGAATCTTAA >SEQ1.fasta ATGGCTCCTCCCT TAGAATCTTAG >SEQ2.fasta Unix% plotorf SEQ1.fasta –stop TAA, TAG –out GA.plot & Unix% getorf SEQ1.fasta –minsize 5 –table 0 –find 1 –out GA.getorf &
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UK MRC Human Genome Mapping Project Resource Centre http://www.hgmp.mrc.ac.uk ATGGGTCGTGAAGAGAATGCTCCTCCTTTGGAATCTTAA TACCCAGCACTTCTCTTACGAGGAGGAAACCTTAGAATT Frame -3 Frame -2 Frame -1 Frame 1 Frame 2 Frame 3 Start and stop codons are located according to the instructions to the program, and the area in between start and stop codons
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UK MRC Human Genome Mapping Project Resource Centre http://www.hgmp.mrc.ac.uk Indication of full coding sequence? Alternative splice form?
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UK MRC Human Genome Mapping Project Resource Centre http://www.hgmp.mrc.ac.uk >_1 [17 - 37] MLLLWNL >_2 [1 - 36] MGREENAPPLES* Using getorf: (min ORF size = 5) stop codon start methionine
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UK MRC Human Genome Mapping Project Resource Centre http://www.hgmp.mrc.ac.uk Unix% transeq SEQ1.fasta –frame 1 –table 0 –sbegin 4 –send 33 -out GA.fasta & >_1 [17 - 37] MLLLWNL >_2 [1 - 36] MGREENAPPLES* >GA.fasta GREENAPPLES Knowledge procured from the literature suggests that this protein is post-translationally modified to cleave the initial methionine residue
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UK MRC Human Genome Mapping Project Resource Centre http://www.hgmp.mrc.ac.uk Unix% needle GA.fasta A.fasta –gapopen 10 –gapextend 0.5 –matrix EPAM250 & Unix% water GA.fasta A.fasta –gapopen 10 –gapextend 0.5 –matrix EPAM250 & >GA.fasta GREENAPPLES >A.fasta APPLES For a global alignment: For a local alignment: Alignments
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UK MRC Human Genome Mapping Project Resource Centre http://www.hgmp.mrc.ac.uk P 1 0 -3 0 0 -2 -3 -2 -5 6 1 0 -6 -5 0 0 S 1 0 1 0 0 0 1 -3 0 -2 -3 1 2 1 -2 -3 0 0 0 T 1 0 0 -2 0 0 0 -2 0 -3 0 1 3 -5 -3 0 0 0 W -6 2 -4 -7 -8 -5 -7 -3 -5 -2 -3 -4 0 -6 -2 -5 17 0 -6 -5 -6 0 Y -3 -4 -2 -4 0 -5 0 -4 2 7 -5 -3 0 10 -2 -3 -4 0 V 0 -2 -2 4 2 2 0 -6 -2 4 0 B 0 2 3 -4 1 2 0 1 -2 -3 1 -2 -5 0 0 -5 -3 -2 2 2 0 Z 0 0 1 3 -5 3 3 2 -2 -3 0 -2 -5 0 0 -6 -4 -2 2 3 0 X 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 A R N D C Q E G H I L K M F P S T W V B Z X Y A 2 0 0 0 0 1 -2 -4 1 1 1 -6 0 0 0 0 -3 N 0 0 2 2 -4 1 1 0 2 -2 -3 1 -2 -4 1 0 -4 -2 2 1 0 D 0 2 4 -5 2 3 1 1 -2 -4 0 -3 -6 0 0 -7 -2 3 3 0 -4 C -2 -4 -5 12 -5 -3 -2 -6 -5 -4 -3 0 -2 -8 -2 -4 -5 0 0 Q 0 1 1 2 4 2 3 -2 1 -5 0 -2 -5 -2 1 3 0 -4 E 0 1 3 -5 2 4 0 1 -2 -3 0 -2 -5 1 0 -7 -2 2 3 0 -4 G 1 -3 0 1 0 5 -2 -3 -4 -2 -3 -5 1 0 -7 0 0 -5 H 2 2 1 -3 3 1 -2 6 0 0 -3 -2 1 2 0 0 I -2 -3 -2 5 2 1 0 -5 4 -2 0 L -2 -3 -4 -6 -2 -3 -4 -2 2 6 4 2 2 -3 -2 2 -3 0 K 3 1 0 -5 1 0 -2 0 -3 5 0 -5 0 0 -3 -2 1 0 0 -4 M 0 -2 -3 -5 -2 -3 -2 2 4 0 6 0 -4 2 -2 0 -5 0 F -4 -6 -4 -5 -2 1 2 -5 0 9 -3 0 7 R -2 6 0 -4 1 -3 2 -2 -3 3 0 -4 0 0 2 -2 0 0 -4 APPESGREENL S E L P A P 1 -4 0 1 1 Gap Open Penalty = 10 Gap Extension Penalty = 0.5 -401 Using PAM250 matrix Alignments
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UK MRC Human Genome Mapping Project Resource Centre http://www.hgmp.mrc.ac.uk P 1 0 -3 0 0 -2 -3 -2 -5 6 1 0 -6 -5 0 0 S 1 0 1 0 0 0 1 -3 0 -2 -3 1 2 1 -2 -3 0 0 0 T 1 0 0 -2 0 0 0 -2 0 -3 0 1 3 -5 -3 0 0 0 W -6 2 -4 -7 -8 -5 -7 -3 -5 -2 -3 -4 0 -6 -2 -5 17 0 -6 -5 -6 0 Y -3 -4 -2 -4 0 -5 0 -4 2 7 -5 -3 0 10 -2 -3 -4 0 V 0 -2 -2 4 2 2 0 -6 -2 4 0 B 0 2 3 -4 1 2 0 1 -2 -3 1 -2 -5 0 0 -5 -3 -2 2 2 0 Z 0 0 1 3 -5 3 3 2 -2 -3 0 -2 -5 0 0 -6 -4 -2 2 3 0 X 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 A R N D C Q E G H I L K M F P S T W V B Z X Y A 2 0 0 0 0 1 -2 -4 1 1 1 -6 0 0 0 0 -3 N 0 0 2 2 -4 1 1 0 2 -2 -3 1 -2 -4 1 0 -4 -2 2 1 0 D 0 2 4 -5 2 3 1 1 -2 -4 0 -3 -6 0 0 -7 -2 3 3 0 -4 C -2 -4 -5 12 -5 -3 -2 -6 -5 -4 -3 0 -2 -8 -2 -4 -5 0 0 Q 0 1 1 2 4 2 3 -2 1 -5 0 -2 -5 -2 1 3 0 -4 E 0 1 3 -5 2 4 0 1 -2 -3 0 -2 -5 1 0 -7 -2 2 3 0 -4 G 1 -3 0 1 0 5 -2 -3 -4 -2 -3 -5 1 0 -7 0 0 -5 H 2 2 1 -3 3 1 -2 6 0 0 -3 -2 1 2 0 0 I -2 -3 -2 5 2 1 0 -5 4 -2 0 L -2 -3 -4 -6 -2 -3 -4 -2 2 6 4 2 2 -3 -2 2 -3 0 K 3 1 0 -5 1 0 -2 0 -3 5 0 -5 0 0 -3 -2 1 0 0 -4 M 0 -2 -3 -5 -2 -3 -2 2 4 0 6 0 -4 2 -2 0 -5 0 F -4 -6 -4 -5 -2 1 2 -5 0 9 -3 0 7 R -2 6 0 -4 1 -3 2 -2 -3 3 0 -4 0 0 2 -2 0 0 -4 APPESGREENL S E L P A P 1 -4 0 1 0001111-302 0 0 0 1 1 1 1 0 2 Gap Open Penalty = 10 Gap Extension Penalty = 0.5 Alignments
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UK MRC Human Genome Mapping Project Resource Centre http://www.hgmp.mrc.ac.uk P 1 0 -3 0 0 -2 -3 -2 -5 6 1 0 -6 -5 0 0 S 1 0 1 0 0 0 1 -3 0 -2 -3 1 2 1 -2 -3 0 0 0 T 1 0 0 -2 0 0 0 -2 0 -3 0 1 3 -5 -3 0 0 0 W -6 2 -4 -7 -8 -5 -7 -3 -5 -2 -3 -4 0 -6 -2 -5 17 0 -6 -5 -6 0 Y -3 -4 -2 -4 0 -5 0 -4 2 7 -5 -3 0 10 -2 -3 -4 0 V 0 -2 -2 4 2 2 0 -6 -2 4 0 B 0 2 3 -4 1 2 0 1 -2 -3 1 -2 -5 0 0 -5 -3 -2 2 2 0 Z 0 0 1 3 -5 3 3 2 -2 -3 0 -2 -5 0 0 -6 -4 -2 2 3 0 X 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 A R N D C Q E G H I L K M F P S T W V B Z X Y A 2 0 0 0 0 1 -2 -4 1 1 1 -6 0 0 0 0 -3 N 0 0 2 2 -4 1 1 0 2 -2 -3 1 -2 -4 1 0 -4 -2 2 1 0 D 0 2 4 -5 2 3 1 1 -2 -4 0 -3 -6 0 0 -7 -2 3 3 0 -4 C -2 -4 -5 12 -5 -3 -2 -6 -5 -4 -3 0 -2 -8 -2 -4 -5 0 0 Q 0 1 1 2 4 2 3 -2 1 -5 0 -2 -5 -2 1 3 0 -4 E 0 1 3 -5 2 4 0 1 -2 -3 0 -2 -5 1 0 -7 -2 2 3 0 -4 G 1 -3 0 1 0 5 -2 -3 -4 -2 -3 -5 1 0 -7 0 0 -5 H 2 2 1 -3 3 1 -2 6 0 0 -3 -2 1 2 0 0 I -2 -3 -2 5 2 1 0 -5 4 -2 0 L -2 -3 -4 -6 -2 -3 -4 -2 2 6 4 2 2 -3 -2 2 -3 0 K 3 1 0 -5 1 0 -2 0 -3 5 0 -5 0 0 -3 -2 1 0 0 -4 M 0 -2 -3 -5 -2 -3 -2 2 4 0 6 0 -4 2 -2 0 -5 0 F -4 -6 -4 -5 -2 1 2 -5 0 9 -3 0 7 R -2 6 0 -4 1 -3 2 -2 -3 3 0 -4 0 0 2 -2 0 0 -4 APPESGREENL S E L P A P 1 -4 0 1 0001111-302 Gap Open Penalty = 10 Gap Extension Penalty = 0.5 0 0 Alignments
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UK MRC Human Genome Mapping Project Resource Centre http://www.hgmp.mrc.ac.uk P 1 0 -3 0 0 -2 -3 -2 -5 6 1 0 -6 -5 0 0 S 1 0 1 0 0 0 1 -3 0 -2 -3 1 2 1 -2 -3 0 0 0 T 1 0 0 -2 0 0 0 -2 0 -3 0 1 3 -5 -3 0 0 0 W -6 2 -4 -7 -8 -5 -7 -3 -5 -2 -3 -4 0 -6 -2 -5 17 0 -6 -5 -6 0 Y -3 -4 -2 -4 0 -5 0 -4 2 7 -5 -3 0 10 -2 -3 -4 0 V 0 -2 -2 4 2 2 0 -6 -2 4 0 B 0 2 3 -4 1 2 0 1 -2 -3 1 -2 -5 0 0 -5 -3 -2 2 2 0 Z 0 0 1 3 -5 3 3 2 -2 -3 0 -2 -5 0 0 -6 -4 -2 2 3 0 X 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 A R N D C Q E G H I L K M F P S T W V B Z X Y A 2 0 0 0 0 1 -2 -4 1 1 1 -6 0 0 0 0 -3 N 0 0 2 2 -4 1 1 0 2 -2 -3 1 -2 -4 1 0 -4 -2 2 1 0 D 0 2 4 -5 2 3 1 1 -2 -4 0 -3 -6 0 0 -7 -2 3 3 0 -4 C -2 -4 -5 12 -5 -3 -2 -6 -5 -4 -3 0 -2 -8 -2 -4 -5 0 0 Q 0 1 1 2 4 2 3 -2 1 -5 0 -2 -5 -2 1 3 0 -4 E 0 1 3 -5 2 4 0 1 -2 -3 0 -2 -5 1 0 -7 -2 2 3 0 -4 G 1 -3 0 1 0 5 -2 -3 -4 -2 -3 -5 1 0 -7 0 0 -5 H 2 2 1 -3 3 1 -2 6 0 0 -3 -2 1 2 0 0 I -2 -3 -2 5 2 1 0 -5 4 -2 0 L -2 -3 -4 -6 -2 -3 -4 -2 2 6 4 2 2 -3 -2 2 -3 0 K 3 1 0 -5 1 0 -2 0 -3 5 0 -5 0 0 -3 -2 1 0 0 -4 M 0 -2 -3 -5 -2 -3 -2 2 4 0 6 0 -4 2 -2 0 -5 0 F -4 -6 -4 -5 -2 1 2 -5 0 9 -3 0 7 R -2 6 0 -4 1 -3 2 -2 -3 3 0 -4 0 0 2 -2 0 0 -4 APPESGREENL S E L P A P 1 -4 0 1 0001111-302 Gap Open Penalty = 10 Gap Extension Penalty = 0.5 1 Alignments
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UK MRC Human Genome Mapping Project Resource Centre http://www.hgmp.mrc.ac.uk P 1 0 -3 0 0 -2 -3 -2 -5 6 1 0 -6 -5 0 0 S 1 0 1 0 0 0 1 -3 0 -2 -3 1 2 1 -2 -3 0 0 0 T 1 0 0 -2 0 0 0 -2 0 -3 0 1 3 -5 -3 0 0 0 W -6 2 -4 -7 -8 -5 -7 -3 -5 -2 -3 -4 0 -6 -2 -5 17 0 -6 -5 -6 0 Y -3 -4 -2 -4 0 -5 0 -4 2 7 -5 -3 0 10 -2 -3 -4 0 V 0 -2 -2 4 2 2 0 -6 -2 4 0 B 0 2 3 -4 1 2 0 1 -2 -3 1 -2 -5 0 0 -5 -3 -2 2 2 0 Z 0 0 1 3 -5 3 3 2 -2 -3 0 -2 -5 0 0 -6 -4 -2 2 3 0 X 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 A R N D C Q E G H I L K M F P S T W V B Z X Y A 2 0 0 0 0 1 -2 -4 1 1 1 -6 0 0 0 0 -3 N 0 0 2 2 -4 1 1 0 2 -2 -3 1 -2 -4 1 0 -4 -2 2 1 0 D 0 2 4 -5 2 3 1 1 -2 -4 0 -3 -6 0 0 -7 -2 3 3 0 -4 C -2 -4 -5 12 -5 -3 -2 -6 -5 -4 -3 0 -2 -8 -2 -4 -5 0 0 Q 0 1 1 2 4 2 3 -2 1 -5 0 -2 -5 -2 1 3 0 -4 E 0 1 3 -5 2 4 0 1 -2 -3 0 -2 -5 1 0 -7 -2 2 3 0 -4 G 1 -3 0 1 0 5 -2 -3 -4 -2 -3 -5 1 0 -7 0 0 -5 H 2 2 1 -3 3 1 -2 6 0 0 -3 -2 1 2 0 0 I -2 -3 -2 5 2 1 0 -5 4 -2 0 L -2 -3 -4 -6 -2 -3 -4 -2 2 6 4 2 2 -3 -2 2 -3 0 K 3 1 0 -5 1 0 -2 0 -3 5 0 -5 0 0 -3 -2 1 0 0 -4 M 0 -2 -3 -5 -2 -3 -2 2 4 0 6 0 -4 2 -2 0 -5 0 F -4 -6 -4 -5 -2 1 2 -5 0 9 -3 0 7 R -2 6 0 -4 1 -3 2 -2 -3 3 0 -4 0 0 2 -2 0 0 -4 APPESGREENL S E L P A P 1 -4 0 1 0001111-302 Gap Open Penalty = 10 Gap Extension Penalty = 0.5 1 0 0 Alignments
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UK MRC Human Genome Mapping Project Resource Centre http://www.hgmp.mrc.ac.uk P 1 0 -3 0 0 -2 -3 -2 -5 6 1 0 -6 -5 0 0 S 1 0 1 0 0 0 1 -3 0 -2 -3 1 2 1 -2 -3 0 0 0 T 1 0 0 -2 0 0 0 -2 0 -3 0 1 3 -5 -3 0 0 0 W -6 2 -4 -7 -8 -5 -7 -3 -5 -2 -3 -4 0 -6 -2 -5 17 0 -6 -5 -6 0 Y -3 -4 -2 -4 0 -5 0 -4 2 7 -5 -3 0 10 -2 -3 -4 0 V 0 -2 -2 4 2 2 0 -6 -2 4 0 B 0 2 3 -4 1 2 0 1 -2 -3 1 -2 -5 0 0 -5 -3 -2 2 2 0 Z 0 0 1 3 -5 3 3 2 -2 -3 0 -2 -5 0 0 -6 -4 -2 2 3 0 X 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 A R N D C Q E G H I L K M F P S T W V B Z X Y A 2 0 0 0 0 1 -2 -4 1 1 1 -6 0 0 0 0 -3 N 0 0 2 2 -4 1 1 0 2 -2 -3 1 -2 -4 1 0 -4 -2 2 1 0 D 0 2 4 -5 2 3 1 1 -2 -4 0 -3 -6 0 0 -7 -2 3 3 0 -4 C -2 -4 -5 12 -5 -3 -2 -6 -5 -4 -3 0 -2 -8 -2 -4 -5 0 0 Q 0 1 1 2 4 2 3 -2 1 -5 0 -2 -5 -2 1 3 0 -4 E 0 1 3 -5 2 4 0 1 -2 -3 0 -2 -5 1 0 -7 -2 2 3 0 -4 G 1 -3 0 1 0 5 -2 -3 -4 -2 -3 -5 1 0 -7 0 0 -5 H 2 2 1 -3 3 1 -2 6 0 0 -3 -2 1 2 0 0 I -2 -3 -2 5 2 1 0 -5 4 -2 0 L -2 -3 -4 -6 -2 -3 -4 -2 2 6 4 2 2 -3 -2 2 -3 0 K 3 1 0 -5 1 0 -2 0 -3 5 0 -5 0 0 -3 -2 1 0 0 -4 M 0 -2 -3 -5 -2 -3 -2 2 4 0 6 0 -4 2 -2 0 -5 0 F -4 -6 -4 -5 -2 1 2 -5 0 9 -3 0 7 R -2 6 0 -4 1 -3 2 -2 -3 3 0 -4 0 0 2 -2 0 0 -4 APPESGREENL S E L P A P 1 -4 0 1 0001111-302 Gap Open Penalty = 10 Gap Extension Penalty = 0.5 1 Alignments
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UK MRC Human Genome Mapping Project Resource Centre http://www.hgmp.mrc.ac.uk P 1 0 -3 0 0 -2 -3 -2 -5 6 1 0 -6 -5 0 0 S 1 0 1 0 0 0 1 -3 0 -2 -3 1 2 1 -2 -3 0 0 0 T 1 0 0 -2 0 0 0 -2 0 -3 0 1 3 -5 -3 0 0 0 W -6 2 -4 -7 -8 -5 -7 -3 -5 -2 -3 -4 0 -6 -2 -5 17 0 -6 -5 -6 0 Y -3 -4 -2 -4 0 -5 0 -4 2 7 -5 -3 0 10 -2 -3 -4 0 V 0 -2 -2 4 2 2 0 -6 -2 4 0 B 0 2 3 -4 1 2 0 1 -2 -3 1 -2 -5 0 0 -5 -3 -2 2 2 0 Z 0 0 1 3 -5 3 3 2 -2 -3 0 -2 -5 0 0 -6 -4 -2 2 3 0 X 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 A R N D C Q E G H I L K M F P S T W V B Z X Y A 2 0 0 0 0 1 -2 -4 1 1 1 -6 0 0 0 0 -3 N 0 0 2 2 -4 1 1 0 2 -2 -3 1 -2 -4 1 0 -4 -2 2 1 0 D 0 2 4 -5 2 3 1 1 -2 -4 0 -3 -6 0 0 -7 -2 3 3 0 -4 C -2 -4 -5 12 -5 -3 -2 -6 -5 -4 -3 0 -2 -8 -2 -4 -5 0 0 Q 0 1 1 2 4 2 3 -2 1 -5 0 -2 -5 -2 1 3 0 -4 E 0 1 3 -5 2 4 0 1 -2 -3 0 -2 -5 1 0 -7 -2 2 3 0 -4 G 1 -3 0 1 0 5 -2 -3 -4 -2 -3 -5 1 0 -7 0 0 -5 H 2 2 1 -3 3 1 -2 6 0 0 -3 -2 1 2 0 0 I -2 -3 -2 5 2 1 0 -5 4 -2 0 L -2 -3 -4 -6 -2 -3 -4 -2 2 6 4 2 2 -3 -2 2 -3 0 K 3 1 0 -5 1 0 -2 0 -3 5 0 -5 0 0 -3 -2 1 0 0 -4 M 0 -2 -3 -5 -2 -3 -2 2 4 0 6 0 -4 2 -2 0 -5 0 F -4 -6 -4 -5 -2 1 2 -5 0 9 -3 0 7 R -2 6 0 -4 1 -3 2 -2 -3 3 0 -4 0 0 2 -2 0 0 -4 APPESGREENL S E L P A P 1 -4 0 1 0001111-302 Gap Open Penalty = 10 Gap Extension Penalty = 0.5 1 0 -9Alignments
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UK MRC Human Genome Mapping Project Resource Centre http://www.hgmp.mrc.ac.uk P 1 0 -3 0 0 -2 -3 -2 -5 6 1 0 -6 -5 0 0 S 1 0 1 0 0 0 1 -3 0 -2 -3 1 2 1 -2 -3 0 0 0 T 1 0 0 -2 0 0 0 -2 0 -3 0 1 3 -5 -3 0 0 0 W -6 2 -4 -7 -8 -5 -7 -3 -5 -2 -3 -4 0 -6 -2 -5 17 0 -6 -5 -6 0 Y -3 -4 -2 -4 0 -5 0 -4 2 7 -5 -3 0 10 -2 -3 -4 0 V 0 -2 -2 4 2 2 0 -6 -2 4 0 B 0 2 3 -4 1 2 0 1 -2 -3 1 -2 -5 0 0 -5 -3 -2 2 2 0 Z 0 0 1 3 -5 3 3 2 -2 -3 0 -2 -5 0 0 -6 -4 -2 2 3 0 X 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 A R N D C Q E G H I L K M F P S T W V B Z X Y A 2 0 0 0 0 1 -2 -4 1 1 1 -6 0 0 0 0 -3 N 0 0 2 2 -4 1 1 0 2 -2 -3 1 -2 -4 1 0 -4 -2 2 1 0 D 0 2 4 -5 2 3 1 1 -2 -4 0 -3 -6 0 0 -7 -2 3 3 0 -4 C -2 -4 -5 12 -5 -3 -2 -6 -5 -4 -3 0 -2 -8 -2 -4 -5 0 0 Q 0 1 1 2 4 2 3 -2 1 -5 0 -2 -5 -2 1 3 0 -4 E 0 1 3 -5 2 4 0 1 -2 -3 0 -2 -5 1 0 -7 -2 2 3 0 -4 G 1 -3 0 1 0 5 -2 -3 -4 -2 -3 -5 1 0 -7 0 0 -5 H 2 2 1 -3 3 1 -2 6 0 0 -3 -2 1 2 0 0 I -2 -3 -2 5 2 1 0 -5 4 -2 0 L -2 -3 -4 -6 -2 -3 -4 -2 2 6 4 2 2 -3 -2 2 -3 0 K 3 1 0 -5 1 0 -2 0 -3 5 0 -5 0 0 -3 -2 1 0 0 -4 M 0 -2 -3 -5 -2 -3 -2 2 4 0 6 0 -4 2 -2 0 -5 0 F -4 -6 -4 -5 -2 1 2 -5 0 9 -3 0 7 R -2 6 0 -4 1 -3 2 -2 -3 3 0 -4 0 0 2 -2 0 0 -4 APPESGREENL S E L P A P 1 -4 0 1 0001111-302 Gap Open Penalty = 10 Gap Extension Penalty = 0.5 1 Alignments
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UK MRC Human Genome Mapping Project Resource Centre http://www.hgmp.mrc.ac.uk P 1 0 -3 0 0 -2 -3 -2 -5 6 1 0 -6 -5 0 0 S 1 0 1 0 0 0 1 -3 0 -2 -3 1 2 1 -2 -3 0 0 0 T 1 0 0 -2 0 0 0 -2 0 -3 0 1 3 -5 -3 0 0 0 W -6 2 -4 -7 -8 -5 -7 -3 -5 -2 -3 -4 0 -6 -2 -5 17 0 -6 -5 -6 0 Y -3 -4 -2 -4 0 -5 0 -4 2 7 -5 -3 0 10 -2 -3 -4 0 V 0 -2 -2 4 2 2 0 -6 -2 4 0 B 0 2 3 -4 1 2 0 1 -2 -3 1 -2 -5 0 0 -5 -3 -2 2 2 0 Z 0 0 1 3 -5 3 3 2 -2 -3 0 -2 -5 0 0 -6 -4 -2 2 3 0 X 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 A R N D C Q E G H I L K M F P S T W V B Z X Y A 2 0 0 0 0 1 -2 -4 1 1 1 -6 0 0 0 0 -3 N 0 0 2 2 -4 1 1 0 2 -2 -3 1 -2 -4 1 0 -4 -2 2 1 0 D 0 2 4 -5 2 3 1 1 -2 -4 0 -3 -6 0 0 -7 -2 3 3 0 -4 C -2 -4 -5 12 -5 -3 -2 -6 -5 -4 -3 0 -2 -8 -2 -4 -5 0 0 Q 0 1 1 2 4 2 3 -2 1 -5 0 -2 -5 -2 1 3 0 -4 E 0 1 3 -5 2 4 0 1 -2 -3 0 -2 -5 1 0 -7 -2 2 3 0 -4 G 1 -3 0 1 0 5 -2 -3 -4 -2 -3 -5 1 0 -7 0 0 -5 H 2 2 1 -3 3 1 -2 6 0 0 -3 -2 1 2 0 0 I -2 -3 -2 5 2 1 0 -5 4 -2 0 L -2 -3 -4 -6 -2 -3 -4 -2 2 6 4 2 2 -3 -2 2 -3 0 K 3 1 0 -5 1 0 -2 0 -3 5 0 -5 0 0 -3 -2 1 0 0 -4 M 0 -2 -3 -5 -2 -3 -2 2 4 0 6 0 -4 2 -2 0 -5 0 F -4 -6 -4 -5 -2 1 2 -5 0 9 -3 0 7 R -2 6 0 -4 1 -3 2 -2 -3 3 0 -4 0 0 2 -2 0 0 -4 Gap Open Penalty = 10 Gap Extension Penalty = 0.5 APPESGREENL S E L P A P 1 -4 0 1 0001111-302 1 -4 -5 0 0 -4 0 0 -2 -3 0 1 -2 -5 -2 1 2 -4 -5 -3 7 9 -4 -5 -4 7 13 6 -5 -4 -2 4 18 5 -8 -4 -6 22 6 1 -3 -9 -2 24 Alignments
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UK MRC Human Genome Mapping Project Resource Centre http://www.hgmp.mrc.ac.uk Alignments To align two or more sequences in a biologically significant way. GREENAPPLES APPLES Local (water) Global (needle) Gap penalty = 10; Extension penalty = 0.5 APPLES
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UK MRC Human Genome Mapping Project Resource Centre http://www.hgmp.mrc.ac.uk GREENAPPLES APPLES looks like the “apples” motif may be part of a larger domain APPLES physicochemical properties pattern searching
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UK MRC Human Genome Mapping Project Resource Centre http://www.hgmp.mrc.ac.uk Physico- chemical properties Unix% iep GA.fasta –plot -step 0.5 –out GA.IEP & Unix% pepinfo GA.fasta –hwindow 8 –generalplot –hydropathyplot & Isoelectric point General properties
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UK MRC Human Genome Mapping Project Resource Centre http://www.hgmp.mrc.ac.uk Physico- chemical properties D Y FW H K R E Q N M A G C S P I V L T Aliphatic Aromatic Hydrophobic Tiny Small Charged Positive Polar The pepinfo graph of properties is based on this diagram
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UK MRC Human Genome Mapping Project Resource Centre http://www.hgmp.mrc.ac.uk Physico- chemical properties non-polar region with small residues polar region to one side of non- charged region
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UK MRC Human Genome Mapping Project Resource Centre http://www.hgmp.mrc.ac.uk Hydropathy plot I 4.50 C 2.50 A 1.80 M 1.90 R-4.50 K-3.90 D-3.50 Q-3.50 N-3.50 E-3.50 H-3.20 S-0.80 T-0.70 P -1.60 Y -1.30 G -0.40 W -0.90 L 3.80 V 4.20 F 2.80 Kyte & Doolittle GREENAPPLES window size = 5 -0.4-4.5-3.5 ++++ = -15.4 5 hydropathy value = -3.08
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UK MRC Human Genome Mapping Project Resource Centre http://www.hgmp.mrc.ac.uk GREENAPPLES 0 Hydropathy plot -3.0 -2.0 -1.5 -2.5 GREEN REENA EENAP ENAPP NAPPL PPLES APPLE no truly hydropathic regions window size = 5
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UK MRC Human Genome Mapping Project Resource Centre http://www.hgmp.mrc.ac.uk Pattern searching GREENAPPL---ES -RE-DAPPL---ES GREEN---LEAVES -RE-D---LEAVES GREENAPPLES >GA.fasta GREENLEAVES >GL.fasta REDAPPLES >RA.fasta REDLEAVES >RL.fasta [G] (0,1)-R–[E] (1,2)–[ND]–X (3)–L–X (3) – E – S
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UK MRC Human Genome Mapping Project Resource Centre http://www.hgmp.mrc.ac.uk Pattern searching Unix% fuzzpro sptr:* pattern.fruit –mismatch 0 –out GA.fuzzpro & Search a protein database: [G] (0,1) - [R] – [E] (1,2) – [ND] –x (3) – [L] –x (3) – [E] – [S] pattern.fruit Nothing resembling this pattern is found in the database - But we could try scanning PRINTS (pscan) and PROSTIE (patmatmotifs) with one of our sequences.
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