Biol 478/595 Intro to Bioinformatics

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1 Biol 478/595 Intro to Bioinformatics September M 1 Labor Day 4 W 3 MG Database Searching Ch. 6 5 F 5 MG Database Searching Hw1 6 M 8 MG Scoring Matrices Ch 3 and Ch 4 7 W 10 MG Pairwise Alignment 8 F 12 MG Pairwise Alignment Hw2 9 M 15 MG Pairwise Alignment Ch W 17 MG Genome Sequencing 1 F 19 MG Gene Finding/Annotation ti Hw3 1 1 M 22 MG Gene Finding/Annotation Ch W 24 MG Sequence Motifs Ch. 7 1 F 26 MG Sequence Motifs Hw4 4 X M 29 Bot h Exam Note modification to reading: Ch 11 genome analysis 1 19-Sep-08

2 Assembly Protocols (Algorithms) Greedy Original method, not used much now Assemble best overlaps first Uses only local information no mate-pair or other map information 2 19-Sep-08

3 Overlap-Layout-Consensus Primary method used today Find all overlaps Layout as graph, removing redundant information Hamiltonian path - visit each vertex once (NP complete) Align and calculate consensus sequence Problems Repeats cause bad overlaps Multiple haplotypes Duplications 3 19-Sep-08

4 Additional Assembly Protocols Comparative assembly - Align to existing very similar to genome Several times faster, at least 3-4X Problems Insertions/deletions Rearrangements Suitable for new HT (short read technologies) Align by physical map Very time and labor intensive 4 19-Sep-08

5 New technologies 454 sequencing DNA is sheared, oligonucleotide adaptors are attached, attached to bead and PCR amplified Nucleotide incorporation releases of inorganic pyrophosphate (PPi) which is detected by luciferase (i.e., light is produced) Each base is added separately. Runs of bases generate more light. Current reads ~ 500 bp SOLiD technology Similar to 454, beads are attached to glass slides Sequence is determined by sequential hybridization and ligation of partially random oligonucleotides with a central determined base (or pair of bases) that is identified by a specific fluorophore. Record color I, cleave and remove ligated oligonucleotide, repeat The reads that are generated are currently 25 bp, but will probably increase to more than 50 bp in the future. Too short for WGS! Good enough for counting RNAs SOLEXA Amplify DNA on a solid surface using fold-back PCR and anchored primers - creates clusters of 1,000 copies of single-stranded DNA molecules. Sequencing using primers, DNA polymerase and four fluorophore-labelled, reversibly terminating nucleotides. Incorporate nucleotide, read color only one base is incorporated Remove terminators, repeat Average read length is currently 40 bp, should increase Too short for WGS! Good enough for counting RNAs 5 19-Sep-08

6 New Sequencing Technologies 454 SOLiD SOLEXA 6 19-Sep-08

7 EST Assembly Assembling RNA Similar to DNA except Contigs do not join into one sequence Sequences are often primarily from one end, e.g., from 3' (poly- A) end Special Artifacts Post-transcriptional modification Alternative splicing Trans-splicing SNPs/haplotypes Chimeras 7 19-Sep-08

8 Populus Science Sep 15;313(5793): Mb (cytogenetic estimate 550 Mb) 2447 major scaffolds containing 410 Mb 19 known chromosomes Remaining 75 Mb mostly repeated, consistent with estimate of 30% heterchromatin 95% of known genes found 45,500 "genes" 155 scaffolds (335 Mb of sequence) mapped to microsattelite markers Evidence for two whole genome duplications 8 19-Sep-08

9 Populus Clone and sequence statistics, note Proportion of small, medium large clones Amount of sequence trimmed Insert Size Kb Vector Number Reads x10-6 Number Reads Number Bases Used Qual > 20 x10-6 Mb Number Bases After Trimming % Bases Used % of Total Mb plasmid plasmid fosmid 0, Total

10 Populus assembly quality Look for chimeric reads Functional definition: include chloroplast, one end nuclear Average 410 reads/position ~5% chimeric Sep-08

11 Populus Unique (no hits) assembles better than repeats Non-redundant (BLAST hits, probably not poplar) assembles poorly Chloroplast and mitochondrial sequence assembles as separate scaffolds Sep-08

12 Fingerprint i clone and contig layout on assembly of LGII 1. (black): clone coverage - each concentric circle represents 5X clone depth. 2. (red): coverage of clones not assigned to contigs (singletons). 3. anchored contigs, alternating ti color scheme. 4. position of clones in contigs, colored by contig assignment. 5. position of clones with no contig assignment. 6. coverage provided by singletons Sep-08 alternating black and white strips = 1Mb

13 Populus Mapping BACs to chromosomes using FISH Also mapped using microsatellite markers Sep-08

14 Populus Transposable Elements LINES (long interspersed repetitive elements) typically retrotransposons, flanked by long terminal (direct) repeats or LTRs. ~20% of mammalian DNA, Copia, Gypsy, etc Contain genes for transposition Disrupt genes causing mutations Transposition RNA polymerase II transcribes the L1 DNA into RNA. The RNA is translated by ribosomes in the cytoplasm into the proteins. The proteins and RNA join together and reenter the nucleus. The endonuclease cuts a strand of "target" DNA, often in the intron of a gene. The reverse transcriptase copies the L1 RNA into L1 DNA which is inserted into the target DNA forming a new L1 element there. SINES (short interspersed repetitive elements), 10-15% of mammalian DNA, non LTR retrotransposons reverse-transcribed RNA molecules originally transcribed b Do not include transposition enzymes Insertion known to cause certain mutations/genetic diseases: Hemophilia A and B (Factor VIII and IX genes), X-linked severe combined immunodeficiency (SCID) (IL-2 receptor), porphyria, predisposition to colon polyps and cancer (APC gene), Duchenne muscular dystrophy (dystrophin gene) MITES (miniature Inverted-repeatrepeat transposable elements) 5' GGCCAGTCACAATGG..~400 nt..ccattgtgactggcc 3' 3' CCGGTCAGTGTTACC..~400 nt..ggtaacactgaccgg 5' ~ bp terminal inverted repeats related to transposons prominent in plants but found in most organisms known to cause mutations Sep-08

15 Populus Whole genome duplication 4DTV distance four-fold degenerate (synonomous) third-codon position transversion in 4 and 6 codon families, the third does not change the corresponding amino acid in WGD all genes are duplicated at same time and therefore tend to have similar 4DTV Sep-08