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Apollo Progress Report PowerPoint PPT Presentation

Apollo Progress Report - ... Run as standalone application or launch from Apollo Load/layer raw analysis results: BLAST (all flavors) sim4 GENSCAN FgenesH Coming soon: BLAT ...

... Run as standalone application or launch from Apollo Load/layer raw analysis results: BLAST (all flavors) sim4 GENSCAN FgenesH Coming soon: BLAT ...

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Multiple-Alignment PowerPoint PPT Presentation

Multiple-Alignment - ... Efficient Tools for Large-Scale Multiple Alignment of Genomic DNA ... Visualizing Interpreting the results The multiple ... data sets that can ...

... Efficient Tools for Large-Scale Multiple Alignment of Genomic DNA ... Visualizing Interpreting the results The multiple ... data sets that can ...

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SRB Genome - a. Broughton et al. (2003) Beans (Phaseolus spp.) model ... (Brassicaceae Repeats) (Fabaceae Repeats) http://plantrepeats.plantbiology.msu.edu/search.html ...

a. Broughton et al. (2003) Beans (Phaseolus spp.) model ... (Brassicaceae Repeats) (Fabaceae Repeats) http://plantrepeats.plantbiology.msu.edu/search.html ...

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Locating markers from the genetic to the physical rice map PowerPoint PPT Presentation

Locating markers from the genetic to the physical rice map - Locating markers from the genetic to the physical rice map Review: Linkage map of molecular markers (Genetic maps) A physical map of the rice genome that is aligned ...

Locating markers from the genetic to the physical rice map Review: Linkage map of molecular markers (Genetic maps) A physical map of the rice genome that is aligned ...

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Annotation de s PowerPoint PPT Presentation

Annotation de s - Olivier Garsmeur Ga tan Droc Franc-Christophe Baurens Dominique This St phanie Sidib -Bocs Annotation de s quences g nomiques: g nes * Before to annotate the ...

Olivier Garsmeur Ga tan Droc Franc-Christophe Baurens Dominique This St phanie Sidib -Bocs Annotation de s quences g nomiques: g nes * Before to annotate the ...

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CS273A Computational Tour of the Human Genome, Gill Bejerano, Spring 2006/07 PowerPoint PPT Presentation

CS273A Computational Tour of the Human Genome, Gill Bejerano, Spring 2006/07 - Profs: Serafim Batzoglou, Gill Bejerano TAs: George Asimenos, Cory McLean http://cs273a.stanford.edu [Bejerano Spr06/07]*

Profs: Serafim Batzoglou, Gill Bejerano TAs: George Asimenos, Cory McLean http://cs273a.stanford.edu [Bejerano Spr06/07]*

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Genome Annotation PowerPoint PPT Presentation

Genome Annotation - Genome Annotation Mark D. Adams Dept. of Genetics 9/10/04 markadams@case.edu Cells, Chromosomes, DNA, and Genes Definitions Unless otherwise stated, annotation refers ...

Genome Annotation Mark D. Adams Dept. of Genetics 9/10/04 markadams@case.edu Cells, Chromosomes, DNA, and Genes Definitions Unless otherwise stated, annotation refers ...

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The Medicago truncatula genome: a progress report - The Medicago truncatula genome: a progress report

The Medicago truncatula genome: a progress report

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Bioinformatics Methods and Applications PowerPoint PPT Presentation

Bioinformatics Methods and Applications - Bioinformatics Methods and Applications Dr. Hongyu Zhang Ceres Inc.

Bioinformatics Methods and Applications Dr. Hongyu Zhang Ceres Inc.

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Eukaryotic Gene Finding PowerPoint PPT Presentation

Eukaryotic Gene Finding - On average, a vertebrate gene is about 30KB long. Coding region takes about 1KB ... Esngl single exon (intronless) (translation start - stop codon) ...

On average, a vertebrate gene is about 30KB long. Coding region takes about 1KB ... Esngl single exon (intronless) (translation start - stop codon) ...

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Tale 1: To Identify an Unknown Gene PowerPoint PPT Presentation

Tale 1: To Identify an Unknown Gene - Photos courtesy of www.webshots.com and Peter Smallwood. Observation ... Print GeneMark 2.4 predictions. 7. Click Start GeneMark.hmm. Surrogate Filters ...

Photos courtesy of www.webshots.com and Peter Smallwood. Observation ... Print GeneMark 2.4 predictions. 7. Click Start GeneMark.hmm. Surrogate Filters ...

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Predicting Genes in Eukaryotic Genomes By Computer PowerPoint PPT Presentation

Predicting Genes in Eukaryotic Genomes By Computer - ... Nature Review Genetics, 3 (2002) 698-710 (mostly ... (Sus scrofa) (Fugu rubripes) (Bambyx mori) (Apsis mellifera) ...

... Nature Review Genetics, 3 (2002) 698-710 (mostly ... (Sus scrofa) (Fugu rubripes) (Bambyx mori) (Apsis mellifera) ...

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Tale 1: To Identify an Unknown Gene - Frog's eye view of the jungle (time moving) Frog's eye view of the jungle (time frozen) Frog's eye view of the jungle (through movement filter) Push to restart time ...

Frog's eye view of the jungle (time moving) Frog's eye view of the jungle (time frozen) Frog's eye view of the jungle (through movement filter) Push to restart time ...

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Eukaryotic Gene Finding - catalysis) Some Statistics. On average, a vertebrate gene is about 30KB long ... Exon sizes can vary from double digit numbers to kilobases. An average 5' UTR ...

catalysis) Some Statistics. On average, a vertebrate gene is about 30KB long ... Exon sizes can vary from double digit numbers to kilobases. An average 5' UTR ...

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Assembling and Annotating the Draft Human Genome - Assembling and Annotating the Draft Human Genome

Assembling and Annotating the Draft Human Genome

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Genome Sequencing and Annotation PowerPoint PPT Presentation

Genome Sequencing and Annotation - Ab Initio Gene Discovery. 5' 3' GC box. CAAT. box. GC. box. TATA ... Statistics-based (ab initio) Methods. Ab initio approach predict genes directly using the ...

Ab Initio Gene Discovery. 5' 3' GC box. CAAT. box. GC. box. TATA ... Statistics-based (ab initio) Methods. Ab initio approach predict genes directly using the ...

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The Genome Access Course Genome Analysis - The Genome Access Course Genome Analysis

The Genome Access Course Genome Analysis

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GENE PAIR HAPLOTYPES AND SEQUENCE SAMPLES FROM STRAWBERRY Rosaceae: Multipurpose, transferable resou PowerPoint PPT Presentation

GENE PAIR HAPLOTYPES AND SEQUENCE SAMPLES FROM STRAWBERRY Rosaceae: Multipurpose, transferable resou - GENE PAIR HAPLOTYPES AND SEQUENCE SAMPLES FROM STRAWBERRY (Rosaceae): Multi ... Development and mapping of gene pair haplotype (GPH) loci ...

GENE PAIR HAPLOTYPES AND SEQUENCE SAMPLES FROM STRAWBERRY (Rosaceae): Multi ... Development and mapping of gene pair haplotype (GPH) loci ...

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Outline - RepeatMasker with MIPS REcat Release 4.3 (Deficient in Helitron ... 39,050 genes have homology or orthology and pass both CDS and QLHR. 9/20/09. CSHL. 23 ...

RepeatMasker with MIPS REcat Release 4.3 (Deficient in Helitron ... 39,050 genes have homology or orthology and pass both CDS and QLHR. 9/20/09. CSHL. 23 ...

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Assembling and Annotating the Draft Human Genome - 300,000 BAC Clones Were Digested and Run on Agarose Gels ... first coding exon, introns, middle coding exons, introns, the 3' UTR and 500 ...

300,000 BAC Clones Were Digested and Run on Agarose Gels ... first coding exon, introns, middle coding exons, introns, the 3' UTR and 500 ...

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Outline - RepeatMasker with MIPS REcat Release 4.3 (Deficient in Helitron ... 39,050 genes have homology or orthology and pass both CDS and QLHR. 9/11/09. CSHL. 23 ...

RepeatMasker with MIPS REcat Release 4.3 (Deficient in Helitron ... 39,050 genes have homology or orthology and pass both CDS and QLHR. 9/11/09. CSHL. 23 ...

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Aucun titre de diapositive PowerPoint PPT Presentation

Aucun titre de diapositive - ... concepts of evolutionary biology in genome annotation. Comparative genomics, concept of orthology and paralogy. What is phylogenomics? ... Orthology/ Paralogy ...

... concepts of evolutionary biology in genome annotation. Comparative genomics, concept of orthology and paralogy. What is phylogenomics? ... Orthology/ Paralogy ...

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Using Expressed Sequence Tags to Improve Gene Structure Prediction PowerPoint PPT Presentation

Using Expressed Sequence Tags to Improve Gene Structure Prediction - Stepping Stone Algorithm and Intron-cutout Algorithm. Genomic Sequence. EST Sequence. Intron Cutout. 21. Result: Mismatches vs. Quality Values ...

Stepping Stone Algorithm and Intron-cutout Algorithm. Genomic Sequence. EST Sequence. Intron Cutout. 21. Result: Mismatches vs. Quality Values ...

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Genomics 101 PowerPoint PPT Presentation

Genomics 101 - Measuring the expression of many genes at a time ... Serge Saxonov. Reading. GENSCAN. EasyGene. SLAM. Twinscan. Optional: Chris Burge's Thesis ...

Measuring the expression of many genes at a time ... Serge Saxonov. Reading. GENSCAN. EasyGene. SLAM. Twinscan. Optional: Chris Burge's Thesis ...

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Assembling and Annotating the Draft Human Genome - ... alignments tend to break at transposon insertions, inversions, duplications, etc. ... Alignments are interrupted by numerous recent transposon insertions. ...

... alignments tend to break at transposon insertions, inversions, duplications, etc. ... Alignments are interrupted by numerous recent transposon insertions. ...

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Finding Genes in the Rice Genome PowerPoint PPT Presentation

Finding Genes in the Rice Genome - Title: Language Theory Combiantiorics and Bioinfromatics Author: aaa Last modified by: Hao Bailin Created Date: 12/4/2001 3:15:40 AM Document presentation format

Title: Language Theory Combiantiorics and Bioinfromatics Author: aaa Last modified by: Hao Bailin Created Date: 12/4/2001 3:15:40 AM Document presentation format

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The Genome Access Course Genome Analysis - The Genome Access Course Genome Analysis

The Genome Access Course Genome Analysis

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Gene%20prediction PowerPoint PPT Presentation

Gene%20prediction - Gene finder. AAAGC ATG CAT TTA ACG A GT GCATC AG GA CTC CAT ACG TAA TGCCG. Fern n Ag ero ... Uno de los gene finders (ab initio) m s precisos ...

Gene finder. AAAGC ATG CAT TTA ACG A GT GCATC AG GA CTC CAT ACG TAA TGCCG. Fern n Ag ero ... Uno de los gene finders (ab initio) m s precisos ...

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Max Bachour - High throughput sequencing technique that can collect a large amount of ... gb|FC457105.1| UCRVU04_CCNI646_g1 Cowpea 524B Mixed Tissue and Conditions cDNA. THK ...

High throughput sequencing technique that can collect a large amount of ... gb|FC457105.1| UCRVU04_CCNI646_g1 Cowpea 524B Mixed Tissue and Conditions cDNA. THK ...

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Gene Prediction PowerPoint PPT Presentation

Gene Prediction - TATA boxes. CAP site. Poly-A. Trained on Arabidopsis ... TATA boxes. Hexamer frequencies. Consensus sequence matching ... Matches TATA box, CCAAT bvox, CpG ...

TATA boxes. CAP site. Poly-A. Trained on Arabidopsis ... TATA boxes. Hexamer frequencies. Consensus sequence matching ... Matches TATA box, CCAAT bvox, CpG ...

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Module 5: Gene prediction PowerPoint PPT Presentation

Module 5: Gene prediction - based on similarity to known genes, or cDNAs ... ICG: TATA-Box predictor. PolyA signal predictors. CSHL: argon.cshl.org/tabaska/polyadq_form.html ...

based on similarity to known genes, or cDNAs ... ICG: TATA-Box predictor. PolyA signal predictors. CSHL: argon.cshl.org/tabaska/polyadq_form.html ...

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Poznanie genomu czlowieka (wg. artykul PowerPoint PPT Presentation

Poznanie genomu czlowieka (wg. artykul - Poznanie genomu cz owieka (wg. artyku w z Science i Nature) Jerzy Tiuryn Instytut Informatyki Uniwersytet Warszawski Dwa artyku y Initial sequencing and ...

Poznanie genomu cz owieka (wg. artyku w z Science i Nature) Jerzy Tiuryn Instytut Informatyki Uniwersytet Warszawski Dwa artyku y Initial sequencing and ...

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Gene Prediction - Use 'gene structure' to predict transcripts and polypeptide (protein) sequences ... Dog MHC class II region so far (Doberman) RefSeq at NCBI ...

Use 'gene structure' to predict transcripts and polypeptide (protein) sequences ... Dog MHC class II region so far (Doberman) RefSeq at NCBI ...

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Evaluating genes and transcripts in Ensembl PowerPoint PPT Presentation

Evaluating genes and transcripts in Ensembl - refined EST matches using EST2GENOME, spangle. Pfam ... Orthology can provide useful confirmation. If no description, check for any Family description ...

refined EST matches using EST2GENOME, spangle. Pfam ... Orthology can provide useful confirmation. If no description, check for any Family description ...

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Genome Annotation - Annotation to identify and describe all the physico-chemical, ... Roche/Boeringer. http://www.expasy.org/cgi-bin/search-biochem-index. EcoCyc. www.ecocyc.org ...

Annotation to identify and describe all the physico-chemical, ... Roche/Boeringer. http://www.expasy.org/cgi-bin/search-biochem-index. EcoCyc. www.ecocyc.org ...

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Protein and Proteome Annotation PowerPoint PPT Presentation

Protein and Proteome Annotation - Objective - identify and describe all the physico-chemical, ... SCOP. http://scop.mrc-lmb.cam.ac.uk/scop/ Lecture 2.5. 20. Expression Databases. Swiss 2D Page ...

Objective - identify and describe all the physico-chemical, ... SCOP. http://scop.mrc-lmb.cam.ac.uk/scop/ Lecture 2.5. 20. Expression Databases. Swiss 2D Page ...

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The challenge of annotating a complete eukaryotic genome: A case study in Drosophila melanogaster PowerPoint PPT Presentation

The challenge of annotating a complete eukaryotic genome: A case study in Drosophila melanogaster - Reese et al., Tutorial #3, ISMB 99. The challenge of annotating a complete eukaryotic genome: ... TATA box. Initiator (Inr) Downstream promoter element (DPE) ...

Reese et al., Tutorial #3, ISMB 99. The challenge of annotating a complete eukaryotic genome: ... TATA box. Initiator (Inr) Downstream promoter element (DPE) ...

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Design and Sources of Annotation PowerPoint PPT Presentation

Design and Sources of Annotation - split gene structure is a general feature. genes can spread over several ... CELLULAR BIOGENESIS. SIGNAL TRANSDUCTION. CELL RESCUE,DEFENSE,CELL DEATH AND AGING ...

split gene structure is a general feature. genes can spread over several ... CELLULAR BIOGENESIS. SIGNAL TRANSDUCTION. CELL RESCUE,DEFENSE,CELL DEATH AND AGING ...

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Genome Bioinformatics PowerPoint PPT Presentation

Genome Bioinformatics - Genome Bioinformatics. Tyler Alioto. Center for Genomic Regulation Barcelona, Spain ... Expressed Sequence (cDNA) or protein sequence available? Yes Spliced alignment ...

Genome Bioinformatics. Tyler Alioto. Center for Genomic Regulation Barcelona, Spain ... Expressed Sequence (cDNA) or protein sequence available? Yes Spliced alignment ...

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Gene Prediction - Chapter 8 Gene Prediction * * * * * * * * * * * * * * * * * * * * * * * * * * * * Automated sequencing of genomes require automated gene assignment Includes detection ...

Chapter 8 Gene Prediction * * * * * * * * * * * * * * * * * * * * * * * * * * * * Automated sequencing of genomes require automated gene assignment Includes detection ...

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Computational Microbiology PowerPoint PPT Presentation

Computational Microbiology - Raise awareness of new kinds of database resources for learning about the ... Supports zoomable, hyperlinked, clickable map views of the genome ...

Raise awareness of new kinds of database resources for learning about the ... Supports zoomable, hyperlinked, clickable map views of the genome ...

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Predictive methods using DNA sequences Unit 11 PowerPoint PPT Presentation

Predictive methods using DNA sequences Unit 11 - Missense type of nonsynonymous (different amino acid in the product of mutated ... COOKY. MONEY. Example of (Positional) Weight Matrix ...

Missense type of nonsynonymous (different amino acid in the product of mutated ... COOKY. MONEY. Example of (Positional) Weight Matrix ...

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Spaghetti Code, Soupy Logic PowerPoint PPT Presentation

Spaghetti Code, Soupy Logic - Simple human/rodent tree. Mutations that occur in rodent ancestor must be counted only once ... rodent. PhyloHMM on Drosophila ...

Simple human/rodent tree. Mutations that occur in rodent ancestor must be counted only once ... rodent. PhyloHMM on Drosophila ...

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Human Annotation the JGI PowerPoint PPT Presentation

Human Annotation the JGI - Manually review high quality evidence (human mRNAs) for which no faithful models ... mouse, rat, chicken, frog, fugu, tetraodon, zebrafish, and drosophila genomes. ...

Manually review high quality evidence (human mRNAs) for which no faithful models ... mouse, rat, chicken, frog, fugu, tetraodon, zebrafish, and drosophila genomes. ...

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1953: Watson and Crick discover the doublehelix nature of DNA PowerPoint PPT Presentation

1953: Watson and Crick discover the doublehelix nature of DNA - 3 letters (triplet a codon) code for one amino acid in a protein. ... For each codon: 3rd column: frequency of usage per thousand ...

3 letters (triplet a codon) code for one amino acid in a protein. ... For each codon: 3rd column: frequency of usage per thousand ...

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Apollo Progress Report - Get alignment sequences for Ensembl data (Have sequences, don't have cigars) ... Suzanna Lewis, Nomi Harris, Mark Gibson, Sima Misra, (John Richter), (Colin Wiel) ...

Get alignment sequences for Ensembl data (Have sequences, don't have cigars) ... Suzanna Lewis, Nomi Harris, Mark Gibson, Sima Misra, (John Richter), (Colin Wiel) ...

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Gene Structure - Gene Structure

Gene Structure

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Course Outline - Course Outline

Course Outline

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Gene PredictionIdentification PowerPoint PPT Presentation

Gene PredictionIdentification - draft. WGS. The hybrid approach. August 2006. The Genome Access Course. Genome Assembly ... Horse. Cat. Mink. Bear. G. Panda. Gibbon. Macaque. Lemur. Tree ...

draft. WGS. The hybrid approach. August 2006. The Genome Access Course. Genome Assembly ... Horse. Cat. Mink. Bear. G. Panda. Gibbon. Macaque. Lemur. Tree ...

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Whole-genome comparative genomics PowerPoint PPT Presentation

Whole-genome comparative genomics - 6.095/6.895 - Computational Biology: Genomes, Networks, Evolution Whole-genome comparative genomics Analyzing the human genome Lecture 21 Dec 6, 2005

6.095/6.895 - Computational Biology: Genomes, Networks, Evolution Whole-genome comparative genomics Analyzing the human genome Lecture 21 Dec 6, 2005

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Identification and Quantification of Polypeptide Similarity Tim PowerPoint PPT Presentation

Identification and Quantification of Polypeptide Similarity Tim - O. aries (domestic sheep) G. gallus (domestic fowl) 1.2Gb ... information is whole genome sequence from a related species, e.g. mouse for man ...

O. aries (domestic sheep) G. gallus (domestic fowl) 1.2Gb ... information is whole genome sequence from a related species, e.g. mouse for man ...

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Overview - TATA box. Initiator. Gene. DNA coding strand. Biological ... upstream regulatory signals (TATA boxes) and local characteristics of the sequence (CpG islands) ...

TATA box. Initiator. Gene. DNA coding strand. Biological ... upstream regulatory signals (TATA boxes) and local characteristics of the sequence (CpG islands) ...

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Gene Finding and HMMs PowerPoint PPT Presentation

Gene Finding and HMMs - Gene Finding and HMMs. Lecture 1 - Introduction. Lecture 2 - Hashing and BLAST ... Lecture 7 - Gene finding and Hidden Markov Models ...

Gene Finding and HMMs. Lecture 1 - Introduction. Lecture 2 - Hashing and BLAST ... Lecture 7 - Gene finding and Hidden Markov Models ...

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Course Outline - Course Outline

Course Outline

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Computational Approaches to Gene Finding PowerPoint PPT Presentation

Computational Approaches to Gene Finding - http://harlequin.jax.org/GenomeAnalysis/hsp53.fa. http: ... Hardest: zebrafish HTGS segment. Tools for Gene Finding Based on Direct or Homology Evidence ...

http://harlequin.jax.org/GenomeAnalysis/hsp53.fa. http: ... Hardest: zebrafish HTGS segment. Tools for Gene Finding Based on Direct or Homology Evidence ...

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Genome Annotation - Uberbacher & Mural PNAS 88:11261, 1991. Neural network. Trained using known gene structures ... Uses descriptions of transcriptional, translational, and ...

Uberbacher & Mural PNAS 88:11261, 1991. Neural network. Trained using known gene structures ... Uses descriptions of transcriptional, translational, and ...

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