alternative splicing prediction -...
TRANSCRIPT
![Page 1: Alternative Splicing Prediction - cs.colostate.eduasa/courses/cs548/fall11/pdfs/splice_grapher.pdf · Fundamentals of Genetics mRNA protein DNA Transcription Translation "Central](https://reader030.vdocuments.us/reader030/viewer/2022041205/5d59f98f88c99304078bc1ee/html5/thumbnails/1.jpg)
Alternative SplicingAlternative SplicingPredictionPrediction
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Fundamentals of Genetics
DNA
"Central Dogma of Molecular Biology"
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Fundamentals of Genetics
mRNA
DNA
Transcription
"Central Dogma of Molecular Biology"
![Page 4: Alternative Splicing Prediction - cs.colostate.eduasa/courses/cs548/fall11/pdfs/splice_grapher.pdf · Fundamentals of Genetics mRNA protein DNA Transcription Translation "Central](https://reader030.vdocuments.us/reader030/viewer/2022041205/5d59f98f88c99304078bc1ee/html5/thumbnails/4.jpg)
Fundamentals of Genetics
mRNA
protein
DNA
TranslationTranscription
"Central Dogma of Molecular Biology"
![Page 5: Alternative Splicing Prediction - cs.colostate.eduasa/courses/cs548/fall11/pdfs/splice_grapher.pdf · Fundamentals of Genetics mRNA protein DNA Transcription Translation "Central](https://reader030.vdocuments.us/reader030/viewer/2022041205/5d59f98f88c99304078bc1ee/html5/thumbnails/5.jpg)
Fundamentals of Genetics
pre-mRNA
![Page 6: Alternative Splicing Prediction - cs.colostate.eduasa/courses/cs548/fall11/pdfs/splice_grapher.pdf · Fundamentals of Genetics mRNA protein DNA Transcription Translation "Central](https://reader030.vdocuments.us/reader030/viewer/2022041205/5d59f98f88c99304078bc1ee/html5/thumbnails/6.jpg)
Fundamentals of Genetics
pre-mRNA
Splicing
mRNA
protein
Translation
![Page 7: Alternative Splicing Prediction - cs.colostate.eduasa/courses/cs548/fall11/pdfs/splice_grapher.pdf · Fundamentals of Genetics mRNA protein DNA Transcription Translation "Central](https://reader030.vdocuments.us/reader030/viewer/2022041205/5d59f98f88c99304078bc1ee/html5/thumbnails/7.jpg)
mRNA SplicingDNA
![Page 8: Alternative Splicing Prediction - cs.colostate.eduasa/courses/cs548/fall11/pdfs/splice_grapher.pdf · Fundamentals of Genetics mRNA protein DNA Transcription Translation "Central](https://reader030.vdocuments.us/reader030/viewer/2022041205/5d59f98f88c99304078bc1ee/html5/thumbnails/8.jpg)
mRNA SplicingDNA
5' 3'
![Page 9: Alternative Splicing Prediction - cs.colostate.eduasa/courses/cs548/fall11/pdfs/splice_grapher.pdf · Fundamentals of Genetics mRNA protein DNA Transcription Translation "Central](https://reader030.vdocuments.us/reader030/viewer/2022041205/5d59f98f88c99304078bc1ee/html5/thumbnails/9.jpg)
pre-mRNA
mRNA SplicingDNA
intronsexons
![Page 10: Alternative Splicing Prediction - cs.colostate.eduasa/courses/cs548/fall11/pdfs/splice_grapher.pdf · Fundamentals of Genetics mRNA protein DNA Transcription Translation "Central](https://reader030.vdocuments.us/reader030/viewer/2022041205/5d59f98f88c99304078bc1ee/html5/thumbnails/10.jpg)
Fundamentals of Genetics
5' 3'
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pre-mRNA
mRNA Splicing
introns
exons
DNA
![Page 12: Alternative Splicing Prediction - cs.colostate.eduasa/courses/cs548/fall11/pdfs/splice_grapher.pdf · Fundamentals of Genetics mRNA protein DNA Transcription Translation "Central](https://reader030.vdocuments.us/reader030/viewer/2022041205/5d59f98f88c99304078bc1ee/html5/thumbnails/12.jpg)
pre-mRNA
mRNA Splicing
mRNA
introns
exons
DNA
![Page 13: Alternative Splicing Prediction - cs.colostate.eduasa/courses/cs548/fall11/pdfs/splice_grapher.pdf · Fundamentals of Genetics mRNA protein DNA Transcription Translation "Central](https://reader030.vdocuments.us/reader030/viewer/2022041205/5d59f98f88c99304078bc1ee/html5/thumbnails/13.jpg)
mRNA Splicing
![Page 14: Alternative Splicing Prediction - cs.colostate.eduasa/courses/cs548/fall11/pdfs/splice_grapher.pdf · Fundamentals of Genetics mRNA protein DNA Transcription Translation "Central](https://reader030.vdocuments.us/reader030/viewer/2022041205/5d59f98f88c99304078bc1ee/html5/thumbnails/14.jpg)
mRNA Splicing
![Page 15: Alternative Splicing Prediction - cs.colostate.eduasa/courses/cs548/fall11/pdfs/splice_grapher.pdf · Fundamentals of Genetics mRNA protein DNA Transcription Translation "Central](https://reader030.vdocuments.us/reader030/viewer/2022041205/5d59f98f88c99304078bc1ee/html5/thumbnails/15.jpg)
pre-mRNApre-mRNA
mRNA mRNA
Alternative Splicing
![Page 16: Alternative Splicing Prediction - cs.colostate.eduasa/courses/cs548/fall11/pdfs/splice_grapher.pdf · Fundamentals of Genetics mRNA protein DNA Transcription Translation "Central](https://reader030.vdocuments.us/reader030/viewer/2022041205/5d59f98f88c99304078bc1ee/html5/thumbnails/16.jpg)
pre-mRNApre-mRNA
mRNA variantsmRNA variants
Alternative Splicing
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Exon Skipping Intron Retention
Alt. 3'Alt. 5' Alt. Both
pre-mRNApre-mRNA
mRNA variantsmRNA variants
Alternative Splicing
![Page 18: Alternative Splicing Prediction - cs.colostate.eduasa/courses/cs548/fall11/pdfs/splice_grapher.pdf · Fundamentals of Genetics mRNA protein DNA Transcription Translation "Central](https://reader030.vdocuments.us/reader030/viewer/2022041205/5d59f98f88c99304078bc1ee/html5/thumbnails/18.jpg)
Why Study Alternative Splicing?
Multiple transcripts
One gene
![Page 19: Alternative Splicing Prediction - cs.colostate.eduasa/courses/cs548/fall11/pdfs/splice_grapher.pdf · Fundamentals of Genetics mRNA protein DNA Transcription Translation "Central](https://reader030.vdocuments.us/reader030/viewer/2022041205/5d59f98f88c99304078bc1ee/html5/thumbnails/19.jpg)
Why Study Alternative Splicing?
Regulation
Multiple transcripts
One gene
![Page 20: Alternative Splicing Prediction - cs.colostate.eduasa/courses/cs548/fall11/pdfs/splice_grapher.pdf · Fundamentals of Genetics mRNA protein DNA Transcription Translation "Central](https://reader030.vdocuments.us/reader030/viewer/2022041205/5d59f98f88c99304078bc1ee/html5/thumbnails/20.jpg)
Why Study Alternative Splicing?
Regulation
Multiple transcripts
One gene
Protein Diversity
![Page 21: Alternative Splicing Prediction - cs.colostate.eduasa/courses/cs548/fall11/pdfs/splice_grapher.pdf · Fundamentals of Genetics mRNA protein DNA Transcription Translation "Central](https://reader030.vdocuments.us/reader030/viewer/2022041205/5d59f98f88c99304078bc1ee/html5/thumbnails/21.jpg)
Why Study Alternative Splicing?
Regulation
Disease
Multiple transcripts
One gene
Protein Diversity
![Page 22: Alternative Splicing Prediction - cs.colostate.eduasa/courses/cs548/fall11/pdfs/splice_grapher.pdf · Fundamentals of Genetics mRNA protein DNA Transcription Translation "Central](https://reader030.vdocuments.us/reader030/viewer/2022041205/5d59f98f88c99304078bc1ee/html5/thumbnails/22.jpg)
Why Study Alternative Splicing?
Regulation
Disease~23,000 genes ~20,000 genes
Multiple transcripts
One gene
Protein Diversity
![Page 23: Alternative Splicing Prediction - cs.colostate.eduasa/courses/cs548/fall11/pdfs/splice_grapher.pdf · Fundamentals of Genetics mRNA protein DNA Transcription Translation "Central](https://reader030.vdocuments.us/reader030/viewer/2022041205/5d59f98f88c99304078bc1ee/html5/thumbnails/23.jpg)
mRNA Sequences
Conventional sequencing● up to full-length mRNA transcripts● costly
mRNA sequence
Genome
![Page 24: Alternative Splicing Prediction - cs.colostate.eduasa/courses/cs548/fall11/pdfs/splice_grapher.pdf · Fundamentals of Genetics mRNA protein DNA Transcription Translation "Central](https://reader030.vdocuments.us/reader030/viewer/2022041205/5d59f98f88c99304078bc1ee/html5/thumbnails/24.jpg)
mRNA Sequences
fl-cDNA
ESTs
![Page 25: Alternative Splicing Prediction - cs.colostate.eduasa/courses/cs548/fall11/pdfs/splice_grapher.pdf · Fundamentals of Genetics mRNA protein DNA Transcription Translation "Central](https://reader030.vdocuments.us/reader030/viewer/2022041205/5d59f98f88c99304078bc1ee/html5/thumbnails/25.jpg)
mRNA Sequences
fl-cDNA
ESTs
![Page 26: Alternative Splicing Prediction - cs.colostate.eduasa/courses/cs548/fall11/pdfs/splice_grapher.pdf · Fundamentals of Genetics mRNA protein DNA Transcription Translation "Central](https://reader030.vdocuments.us/reader030/viewer/2022041205/5d59f98f88c99304078bc1ee/html5/thumbnails/26.jpg)
Gene Models
● Start, end, introns, exons, etc.● “wet-lab” results● computational results (ESTs)
Description of known features
![Page 27: Alternative Splicing Prediction - cs.colostate.eduasa/courses/cs548/fall11/pdfs/splice_grapher.pdf · Fundamentals of Genetics mRNA protein DNA Transcription Translation "Central](https://reader030.vdocuments.us/reader030/viewer/2022041205/5d59f98f88c99304078bc1ee/html5/thumbnails/27.jpg)
RNA-Seq
fl-cDNA
EST
RNA-Seq
"Next-Generation" sequencing● short "reads"● cheap, plentiful
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Ungapped Alignment
mRNA sequence
DNA sequence
TGTTTTTTACCAGGAGTTGCCAAGAATTGGCCAATGCCTTCTTACGACC
GAATTGGCCAATGCCTTCTTAC
GAATTGGCCAATGCCTTCTTAC
![Page 29: Alternative Splicing Prediction - cs.colostate.eduasa/courses/cs548/fall11/pdfs/splice_grapher.pdf · Fundamentals of Genetics mRNA protein DNA Transcription Translation "Central](https://reader030.vdocuments.us/reader030/viewer/2022041205/5d59f98f88c99304078bc1ee/html5/thumbnails/29.jpg)
Spliced Alignment
TGATTCAGTCATCACTTTAAGAGCCATGGAGT
short readshort read
![Page 30: Alternative Splicing Prediction - cs.colostate.eduasa/courses/cs548/fall11/pdfs/splice_grapher.pdf · Fundamentals of Genetics mRNA protein DNA Transcription Translation "Central](https://reader030.vdocuments.us/reader030/viewer/2022041205/5d59f98f88c99304078bc1ee/html5/thumbnails/30.jpg)
Spliced Alignment
TGATTCAGTCATCA .........
TGATTCAGTCATCA
TGATTCAGTCATCACTTTAAGAGCCATGGAGT
short readshort read
Genomic referenceGenomic reference
![Page 31: Alternative Splicing Prediction - cs.colostate.eduasa/courses/cs548/fall11/pdfs/splice_grapher.pdf · Fundamentals of Genetics mRNA protein DNA Transcription Translation "Central](https://reader030.vdocuments.us/reader030/viewer/2022041205/5d59f98f88c99304078bc1ee/html5/thumbnails/31.jpg)
Spliced Alignment
TGATTCAGTCATCA ......... CTTTAAGAGCCATGGAGT
TGATTCAGTCATCA CTTTAAGAGCCATGGAGT
TGATTCAGTCATCACTTTAAGAGCCATGGAGT
short readshort read
Genomic referenceGenomic reference
![Page 32: Alternative Splicing Prediction - cs.colostate.eduasa/courses/cs548/fall11/pdfs/splice_grapher.pdf · Fundamentals of Genetics mRNA protein DNA Transcription Translation "Central](https://reader030.vdocuments.us/reader030/viewer/2022041205/5d59f98f88c99304078bc1ee/html5/thumbnails/32.jpg)
Spliced Alignment
TGATTCAGTCATCA GT.....AG CTTTAAGAGCCATGGAGT
TGATTCAGTCATCA CTTTAAGAGCCATGGAGT
TGATTCAGTCATCACTTTAAGAGCCATGGAGT
short readshort read
Genomic referenceGenomic reference
![Page 33: Alternative Splicing Prediction - cs.colostate.eduasa/courses/cs548/fall11/pdfs/splice_grapher.pdf · Fundamentals of Genetics mRNA protein DNA Transcription Translation "Central](https://reader030.vdocuments.us/reader030/viewer/2022041205/5d59f98f88c99304078bc1ee/html5/thumbnails/33.jpg)
Anchor Regions
TGATTCAGTCATCA GT.....AG CTTTAAGAGCCATGGAGT
TGATTCAGTCATCA CT
Genomic referenceGenomic reference
2nt anchor: P(match by chance) = 1/16
Anchor region: minimum length by which a readoverlaps a junction on either side
![Page 34: Alternative Splicing Prediction - cs.colostate.eduasa/courses/cs548/fall11/pdfs/splice_grapher.pdf · Fundamentals of Genetics mRNA protein DNA Transcription Translation "Central](https://reader030.vdocuments.us/reader030/viewer/2022041205/5d59f98f88c99304078bc1ee/html5/thumbnails/34.jpg)
Anchor Regions
TGATTCAGTCATCA GT.....AG CTTTAAGAGCCATGGAGT
TGATTCAGTCATCA CTTTAAGA
Genomic referenceGenomic reference
8nt anchor: P(match by chance) = 1/48
= 1/65,536
Anchor region: minimum length by which a readoverlaps a junction on either side
![Page 35: Alternative Splicing Prediction - cs.colostate.eduasa/courses/cs548/fall11/pdfs/splice_grapher.pdf · Fundamentals of Genetics mRNA protein DNA Transcription Translation "Central](https://reader030.vdocuments.us/reader030/viewer/2022041205/5d59f98f88c99304078bc1ee/html5/thumbnails/35.jpg)
File Formats
Sequences: FASTQ
![Page 36: Alternative Splicing Prediction - cs.colostate.eduasa/courses/cs548/fall11/pdfs/splice_grapher.pdf · Fundamentals of Genetics mRNA protein DNA Transcription Translation "Central](https://reader030.vdocuments.us/reader030/viewer/2022041205/5d59f98f88c99304078bc1ee/html5/thumbnails/36.jpg)
File Formats
Gene Models: GFF3
![Page 37: Alternative Splicing Prediction - cs.colostate.eduasa/courses/cs548/fall11/pdfs/splice_grapher.pdf · Fundamentals of Genetics mRNA protein DNA Transcription Translation "Central](https://reader030.vdocuments.us/reader030/viewer/2022041205/5d59f98f88c99304078bc1ee/html5/thumbnails/37.jpg)
File Formats
Gene Models: GTF
![Page 38: Alternative Splicing Prediction - cs.colostate.eduasa/courses/cs548/fall11/pdfs/splice_grapher.pdf · Fundamentals of Genetics mRNA protein DNA Transcription Translation "Central](https://reader030.vdocuments.us/reader030/viewer/2022041205/5d59f98f88c99304078bc1ee/html5/thumbnails/38.jpg)
File Formats
Alignments: SAM
![Page 39: Alternative Splicing Prediction - cs.colostate.eduasa/courses/cs548/fall11/pdfs/splice_grapher.pdf · Fundamentals of Genetics mRNA protein DNA Transcription Translation "Central](https://reader030.vdocuments.us/reader030/viewer/2022041205/5d59f98f88c99304078bc1ee/html5/thumbnails/39.jpg)
Splice Graphs vs. Transcripts
Transcripts
![Page 40: Alternative Splicing Prediction - cs.colostate.eduasa/courses/cs548/fall11/pdfs/splice_grapher.pdf · Fundamentals of Genetics mRNA protein DNA Transcription Translation "Central](https://reader030.vdocuments.us/reader030/viewer/2022041205/5d59f98f88c99304078bc1ee/html5/thumbnails/40.jpg)
Splice Graphs vs. Transcripts
Transcripts
fl-cDNA
![Page 41: Alternative Splicing Prediction - cs.colostate.eduasa/courses/cs548/fall11/pdfs/splice_grapher.pdf · Fundamentals of Genetics mRNA protein DNA Transcription Translation "Central](https://reader030.vdocuments.us/reader030/viewer/2022041205/5d59f98f88c99304078bc1ee/html5/thumbnails/41.jpg)
Splice Graphs vs. Transcripts
Splice Graph
Transcripts
fl-cDNA
![Page 42: Alternative Splicing Prediction - cs.colostate.eduasa/courses/cs548/fall11/pdfs/splice_grapher.pdf · Fundamentals of Genetics mRNA protein DNA Transcription Translation "Central](https://reader030.vdocuments.us/reader030/viewer/2022041205/5d59f98f88c99304078bc1ee/html5/thumbnails/42.jpg)
Splice Graphs vs. Transcripts
Splice Graph
Transcripts
fl-cDNA, ESTsRNA-Seq
fl-cDNA
![Page 43: Alternative Splicing Prediction - cs.colostate.eduasa/courses/cs548/fall11/pdfs/splice_grapher.pdf · Fundamentals of Genetics mRNA protein DNA Transcription Translation "Central](https://reader030.vdocuments.us/reader030/viewer/2022041205/5d59f98f88c99304078bc1ee/html5/thumbnails/43.jpg)
SpliceGrapherGene ModelGene Model
![Page 44: Alternative Splicing Prediction - cs.colostate.eduasa/courses/cs548/fall11/pdfs/splice_grapher.pdf · Fundamentals of Genetics mRNA protein DNA Transcription Translation "Central](https://reader030.vdocuments.us/reader030/viewer/2022041205/5d59f98f88c99304078bc1ee/html5/thumbnails/44.jpg)
SpliceGrapher
ESTsESTs
Gene ModelGene Model
![Page 45: Alternative Splicing Prediction - cs.colostate.eduasa/courses/cs548/fall11/pdfs/splice_grapher.pdf · Fundamentals of Genetics mRNA protein DNA Transcription Translation "Central](https://reader030.vdocuments.us/reader030/viewer/2022041205/5d59f98f88c99304078bc1ee/html5/thumbnails/45.jpg)
SpliceGrapher
RNA-SeqRNA-Seq ESTsESTs
Gene ModelGene Model
![Page 46: Alternative Splicing Prediction - cs.colostate.eduasa/courses/cs548/fall11/pdfs/splice_grapher.pdf · Fundamentals of Genetics mRNA protein DNA Transcription Translation "Central](https://reader030.vdocuments.us/reader030/viewer/2022041205/5d59f98f88c99304078bc1ee/html5/thumbnails/46.jpg)
RNA-Seq DataUngapped alignmentsUngapped alignments
Predicted Splice GraphPredicted Splice Graph
![Page 47: Alternative Splicing Prediction - cs.colostate.eduasa/courses/cs548/fall11/pdfs/splice_grapher.pdf · Fundamentals of Genetics mRNA protein DNA Transcription Translation "Central](https://reader030.vdocuments.us/reader030/viewer/2022041205/5d59f98f88c99304078bc1ee/html5/thumbnails/47.jpg)
RNA-Seq DataUngapped alignmentsUngapped alignments
Predicted Splice GraphPredicted Splice Graph
![Page 48: Alternative Splicing Prediction - cs.colostate.eduasa/courses/cs548/fall11/pdfs/splice_grapher.pdf · Fundamentals of Genetics mRNA protein DNA Transcription Translation "Central](https://reader030.vdocuments.us/reader030/viewer/2022041205/5d59f98f88c99304078bc1ee/html5/thumbnails/48.jpg)
RNA-Seq DataUngapped alignmentsUngapped alignments
Spliced AlignmentsSpliced Alignments
Predicted Splice GraphPredicted Splice Graph
![Page 49: Alternative Splicing Prediction - cs.colostate.eduasa/courses/cs548/fall11/pdfs/splice_grapher.pdf · Fundamentals of Genetics mRNA protein DNA Transcription Translation "Central](https://reader030.vdocuments.us/reader030/viewer/2022041205/5d59f98f88c99304078bc1ee/html5/thumbnails/49.jpg)
Spliced AlignmentsSpliced Alignments
RNA-Seq DataUngapped alignmentsUngapped alignments
Predicted Splice GraphPredicted Splice Graph
offset = 14nt
![Page 50: Alternative Splicing Prediction - cs.colostate.eduasa/courses/cs548/fall11/pdfs/splice_grapher.pdf · Fundamentals of Genetics mRNA protein DNA Transcription Translation "Central](https://reader030.vdocuments.us/reader030/viewer/2022041205/5d59f98f88c99304078bc1ee/html5/thumbnails/50.jpg)
Challenges with RNA-Seq
Short Reads
![Page 51: Alternative Splicing Prediction - cs.colostate.eduasa/courses/cs548/fall11/pdfs/splice_grapher.pdf · Fundamentals of Genetics mRNA protein DNA Transcription Translation "Central](https://reader030.vdocuments.us/reader030/viewer/2022041205/5d59f98f88c99304078bc1ee/html5/thumbnails/51.jpg)
Challenges with RNA-Seq
Short Reads
Ambiguous OriginsAmbiguous Origins
![Page 52: Alternative Splicing Prediction - cs.colostate.eduasa/courses/cs548/fall11/pdfs/splice_grapher.pdf · Fundamentals of Genetics mRNA protein DNA Transcription Translation "Central](https://reader030.vdocuments.us/reader030/viewer/2022041205/5d59f98f88c99304078bc1ee/html5/thumbnails/52.jpg)
Challenges with RNA-Seq
Short Reads
Ambiguous OriginsAmbiguous Origins
Variable CoverageVariable Coverage
![Page 53: Alternative Splicing Prediction - cs.colostate.eduasa/courses/cs548/fall11/pdfs/splice_grapher.pdf · Fundamentals of Genetics mRNA protein DNA Transcription Translation "Central](https://reader030.vdocuments.us/reader030/viewer/2022041205/5d59f98f88c99304078bc1ee/html5/thumbnails/53.jpg)
Challenges with RNA-Seq
Short Reads
Ambiguous OriginsAmbiguous Origins
Variable CoverageVariable Coverage
![Page 54: Alternative Splicing Prediction - cs.colostate.eduasa/courses/cs548/fall11/pdfs/splice_grapher.pdf · Fundamentals of Genetics mRNA protein DNA Transcription Translation "Central](https://reader030.vdocuments.us/reader030/viewer/2022041205/5d59f98f88c99304078bc1ee/html5/thumbnails/54.jpg)
Challenges with RNA-Seq
Short Reads
Ambiguous OriginsAmbiguous Origins
Variable CoverageVariable Coverage
![Page 55: Alternative Splicing Prediction - cs.colostate.eduasa/courses/cs548/fall11/pdfs/splice_grapher.pdf · Fundamentals of Genetics mRNA protein DNA Transcription Translation "Central](https://reader030.vdocuments.us/reader030/viewer/2022041205/5d59f98f88c99304078bc1ee/html5/thumbnails/55.jpg)
Challenges with RNA-Seq
Short Reads
Ambiguous OriginsAmbiguous Origins
Variable CoverageVariable Coverage
Highly Localized EvidenceHighly Localized Evidence
![Page 56: Alternative Splicing Prediction - cs.colostate.eduasa/courses/cs548/fall11/pdfs/splice_grapher.pdf · Fundamentals of Genetics mRNA protein DNA Transcription Translation "Central](https://reader030.vdocuments.us/reader030/viewer/2022041205/5d59f98f88c99304078bc1ee/html5/thumbnails/56.jpg)
Validating Splice Sites
Splice SiteSVM
GeneModels
ESTAlignments
![Page 57: Alternative Splicing Prediction - cs.colostate.eduasa/courses/cs548/fall11/pdfs/splice_grapher.pdf · Fundamentals of Genetics mRNA protein DNA Transcription Translation "Central](https://reader030.vdocuments.us/reader030/viewer/2022041205/5d59f98f88c99304078bc1ee/html5/thumbnails/57.jpg)
Validating Splice Sites
Splice SiteSVM
GeneModels
ESTAlignments
Accuracy ~87-97%
![Page 58: Alternative Splicing Prediction - cs.colostate.eduasa/courses/cs548/fall11/pdfs/splice_grapher.pdf · Fundamentals of Genetics mRNA protein DNA Transcription Translation "Central](https://reader030.vdocuments.us/reader030/viewer/2022041205/5d59f98f88c99304078bc1ee/html5/thumbnails/58.jpg)
Validating Splice Sites
Genomic referenceGenomic reference
Splice SiteSVM
TCATGTCTTCATGTTTGCGGTAAGAGGTAGTCATCACTTTAAGAG
GeneModels
ESTAlignments
Accuracy ~87-97%
![Page 59: Alternative Splicing Prediction - cs.colostate.eduasa/courses/cs548/fall11/pdfs/splice_grapher.pdf · Fundamentals of Genetics mRNA protein DNA Transcription Translation "Central](https://reader030.vdocuments.us/reader030/viewer/2022041205/5d59f98f88c99304078bc1ee/html5/thumbnails/59.jpg)
Validating Splice Sites
Genomic referenceGenomic reference
Splice SiteSVM
TCATGTCTTCATGTTTGCGGTAAGAGGTAGTCATCACTTTAAGAG
GeneModels
ESTAlignments
Accuracy ~87-97%
![Page 60: Alternative Splicing Prediction - cs.colostate.eduasa/courses/cs548/fall11/pdfs/splice_grapher.pdf · Fundamentals of Genetics mRNA protein DNA Transcription Translation "Central](https://reader030.vdocuments.us/reader030/viewer/2022041205/5d59f98f88c99304078bc1ee/html5/thumbnails/60.jpg)
Other Approaches
● Splice graph prediction Sircah (EST only)
![Page 61: Alternative Splicing Prediction - cs.colostate.eduasa/courses/cs548/fall11/pdfs/splice_grapher.pdf · Fundamentals of Genetics mRNA protein DNA Transcription Translation "Central](https://reader030.vdocuments.us/reader030/viewer/2022041205/5d59f98f88c99304078bc1ee/html5/thumbnails/61.jpg)
Other Approaches
● Splice graph prediction Sircah (EST only)
● Transcript prediction BowTie/TopHat/Cufflinks HashMatch/Supersplat/TAU Scripture
![Page 62: Alternative Splicing Prediction - cs.colostate.eduasa/courses/cs548/fall11/pdfs/splice_grapher.pdf · Fundamentals of Genetics mRNA protein DNA Transcription Translation "Central](https://reader030.vdocuments.us/reader030/viewer/2022041205/5d59f98f88c99304078bc1ee/html5/thumbnails/62.jpg)
Other Approaches
● Splice graph prediction Sircah (EST only)
● Transcript prediction BowTie/TopHat/Cufflinks HashMatch/Supersplat/TAU Scripture
![Page 63: Alternative Splicing Prediction - cs.colostate.eduasa/courses/cs548/fall11/pdfs/splice_grapher.pdf · Fundamentals of Genetics mRNA protein DNA Transcription Translation "Central](https://reader030.vdocuments.us/reader030/viewer/2022041205/5d59f98f88c99304078bc1ee/html5/thumbnails/63.jpg)
Results
AS Predictions for AS Predictions for A. thalianaA. thaliana
![Page 64: Alternative Splicing Prediction - cs.colostate.eduasa/courses/cs548/fall11/pdfs/splice_grapher.pdf · Fundamentals of Genetics mRNA protein DNA Transcription Translation "Central](https://reader030.vdocuments.us/reader030/viewer/2022041205/5d59f98f88c99304078bc1ee/html5/thumbnails/64.jpg)
Results
AS Predictions for AS Predictions for A. thalianaA. thaliana
![Page 65: Alternative Splicing Prediction - cs.colostate.eduasa/courses/cs548/fall11/pdfs/splice_grapher.pdf · Fundamentals of Genetics mRNA protein DNA Transcription Translation "Central](https://reader030.vdocuments.us/reader030/viewer/2022041205/5d59f98f88c99304078bc1ee/html5/thumbnails/65.jpg)
Results
AS Predictions for AS Predictions for A. thalianaA. thaliana
![Page 66: Alternative Splicing Prediction - cs.colostate.eduasa/courses/cs548/fall11/pdfs/splice_grapher.pdf · Fundamentals of Genetics mRNA protein DNA Transcription Translation "Central](https://reader030.vdocuments.us/reader030/viewer/2022041205/5d59f98f88c99304078bc1ee/html5/thumbnails/66.jpg)
Results
![Page 67: Alternative Splicing Prediction - cs.colostate.eduasa/courses/cs548/fall11/pdfs/splice_grapher.pdf · Fundamentals of Genetics mRNA protein DNA Transcription Translation "Central](https://reader030.vdocuments.us/reader030/viewer/2022041205/5d59f98f88c99304078bc1ee/html5/thumbnails/67.jpg)
Results
![Page 68: Alternative Splicing Prediction - cs.colostate.eduasa/courses/cs548/fall11/pdfs/splice_grapher.pdf · Fundamentals of Genetics mRNA protein DNA Transcription Translation "Central](https://reader030.vdocuments.us/reader030/viewer/2022041205/5d59f98f88c99304078bc1ee/html5/thumbnails/68.jpg)
Results
![Page 69: Alternative Splicing Prediction - cs.colostate.eduasa/courses/cs548/fall11/pdfs/splice_grapher.pdf · Fundamentals of Genetics mRNA protein DNA Transcription Translation "Central](https://reader030.vdocuments.us/reader030/viewer/2022041205/5d59f98f88c99304078bc1ee/html5/thumbnails/69.jpg)
Results
![Page 70: Alternative Splicing Prediction - cs.colostate.eduasa/courses/cs548/fall11/pdfs/splice_grapher.pdf · Fundamentals of Genetics mRNA protein DNA Transcription Translation "Central](https://reader030.vdocuments.us/reader030/viewer/2022041205/5d59f98f88c99304078bc1ee/html5/thumbnails/70.jpg)
Results
![Page 71: Alternative Splicing Prediction - cs.colostate.eduasa/courses/cs548/fall11/pdfs/splice_grapher.pdf · Fundamentals of Genetics mRNA protein DNA Transcription Translation "Central](https://reader030.vdocuments.us/reader030/viewer/2022041205/5d59f98f88c99304078bc1ee/html5/thumbnails/71.jpg)
Example 1 - Cufflinks
![Page 72: Alternative Splicing Prediction - cs.colostate.eduasa/courses/cs548/fall11/pdfs/splice_grapher.pdf · Fundamentals of Genetics mRNA protein DNA Transcription Translation "Central](https://reader030.vdocuments.us/reader030/viewer/2022041205/5d59f98f88c99304078bc1ee/html5/thumbnails/72.jpg)
Example 1 - TAU
![Page 73: Alternative Splicing Prediction - cs.colostate.eduasa/courses/cs548/fall11/pdfs/splice_grapher.pdf · Fundamentals of Genetics mRNA protein DNA Transcription Translation "Central](https://reader030.vdocuments.us/reader030/viewer/2022041205/5d59f98f88c99304078bc1ee/html5/thumbnails/73.jpg)
Example 1 - SpliceGrapher
![Page 74: Alternative Splicing Prediction - cs.colostate.eduasa/courses/cs548/fall11/pdfs/splice_grapher.pdf · Fundamentals of Genetics mRNA protein DNA Transcription Translation "Central](https://reader030.vdocuments.us/reader030/viewer/2022041205/5d59f98f88c99304078bc1ee/html5/thumbnails/74.jpg)
Example 2 - Cufflinks
![Page 75: Alternative Splicing Prediction - cs.colostate.eduasa/courses/cs548/fall11/pdfs/splice_grapher.pdf · Fundamentals of Genetics mRNA protein DNA Transcription Translation "Central](https://reader030.vdocuments.us/reader030/viewer/2022041205/5d59f98f88c99304078bc1ee/html5/thumbnails/75.jpg)
Example 2 - TAU
![Page 76: Alternative Splicing Prediction - cs.colostate.eduasa/courses/cs548/fall11/pdfs/splice_grapher.pdf · Fundamentals of Genetics mRNA protein DNA Transcription Translation "Central](https://reader030.vdocuments.us/reader030/viewer/2022041205/5d59f98f88c99304078bc1ee/html5/thumbnails/76.jpg)
Example 2 - SpliceGrapher
![Page 77: Alternative Splicing Prediction - cs.colostate.eduasa/courses/cs548/fall11/pdfs/splice_grapher.pdf · Fundamentals of Genetics mRNA protein DNA Transcription Translation "Central](https://reader030.vdocuments.us/reader030/viewer/2022041205/5d59f98f88c99304078bc1ee/html5/thumbnails/77.jpg)
Example 3 - Cufflinks
![Page 78: Alternative Splicing Prediction - cs.colostate.eduasa/courses/cs548/fall11/pdfs/splice_grapher.pdf · Fundamentals of Genetics mRNA protein DNA Transcription Translation "Central](https://reader030.vdocuments.us/reader030/viewer/2022041205/5d59f98f88c99304078bc1ee/html5/thumbnails/78.jpg)
Example 3 - TAU
![Page 79: Alternative Splicing Prediction - cs.colostate.eduasa/courses/cs548/fall11/pdfs/splice_grapher.pdf · Fundamentals of Genetics mRNA protein DNA Transcription Translation "Central](https://reader030.vdocuments.us/reader030/viewer/2022041205/5d59f98f88c99304078bc1ee/html5/thumbnails/79.jpg)
Example 3 - SpliceGrapher
![Page 80: Alternative Splicing Prediction - cs.colostate.eduasa/courses/cs548/fall11/pdfs/splice_grapher.pdf · Fundamentals of Genetics mRNA protein DNA Transcription Translation "Central](https://reader030.vdocuments.us/reader030/viewer/2022041205/5d59f98f88c99304078bc1ee/html5/thumbnails/80.jpg)
Conclusions
● Uses gene models, ESTs, and RNA-seq
![Page 81: Alternative Splicing Prediction - cs.colostate.eduasa/courses/cs548/fall11/pdfs/splice_grapher.pdf · Fundamentals of Genetics mRNA protein DNA Transcription Translation "Central](https://reader030.vdocuments.us/reader030/viewer/2022041205/5d59f98f88c99304078bc1ee/html5/thumbnails/81.jpg)
Conclusions
● Uses gene models, ESTs, and RNA-seq● Conservative splice graph predictions
Curated gene models establish context Accurate splice site models
![Page 82: Alternative Splicing Prediction - cs.colostate.eduasa/courses/cs548/fall11/pdfs/splice_grapher.pdf · Fundamentals of Genetics mRNA protein DNA Transcription Translation "Central](https://reader030.vdocuments.us/reader030/viewer/2022041205/5d59f98f88c99304078bc1ee/html5/thumbnails/82.jpg)
Conclusions
● Uses gene models, ESTs, and RNA-seq● Conservative splice graph predictions
Curated gene models establish context Accurate splice site models
● Visualization aids
![Page 83: Alternative Splicing Prediction - cs.colostate.eduasa/courses/cs548/fall11/pdfs/splice_grapher.pdf · Fundamentals of Genetics mRNA protein DNA Transcription Translation "Central](https://reader030.vdocuments.us/reader030/viewer/2022041205/5d59f98f88c99304078bc1ee/html5/thumbnails/83.jpg)
Ongoing Analyses
PlantsA.thaliana V.vinifera B.distachyon G.max O.sativa
MammalsB.taurusH.sapiens
![Page 84: Alternative Splicing Prediction - cs.colostate.eduasa/courses/cs548/fall11/pdfs/splice_grapher.pdf · Fundamentals of Genetics mRNA protein DNA Transcription Translation "Central](https://reader030.vdocuments.us/reader030/viewer/2022041205/5d59f98f88c99304078bc1ee/html5/thumbnails/84.jpg)
More Information
Funding from NSF award 0743097
Sofware: splicegrapher.sourceforge.netResults: http://combi.cs.colostate.edu/SpliceGrapher