Presentation is loading. Please wait.

Presentation is loading. Please wait.

The Scarlet Runner Bean Genome: Contig 230613 By Eden Maloney.

Published byAmos Douglas Modified over 9 years ago

Similar presentations

Presentation on theme: "The Scarlet Runner Bean Genome: Contig 230613 By Eden Maloney."— Presentation transcript:

1 The Scarlet Runner Bean Genome: Contig 230613 By Eden Maloney

2 CONTIG 230613 Part of Scarlet Runner Bean (Phaseolus coccineus) Genome 18, 403 base pairs Two Predicted Genes – Conserved Hypothetical Protein – Known from Soybean: Gylcine Max 2 possibly Repeats

3 FGENESH Length of Genes (bp) BLASTNTBLASTNBLASTPDescription Gene 13968e-736e-27 647 bp 1.1 XP_001096185 PREDICTED: microtubule associated monoxygenase, calponin and LIM domain containing 2 isoform 1 [Macaca mulatta] Gene 2273 6e-53 6e-13161 bp 5e-15 EEF27784 conserved hypothetical protein [Ricinus communis] Gene 3273 5e-23 5e-18 742 bp 2e-09 EEF27117 conserved hypothetical protein [Ricinus communis] Gene 46300.02e- 102 777 bp 6e-115 CAA33227 emb|CAA33227.1|emb|CAA33227.1| unnamed protein product [Glycine max] 416 6e-115 416 Genescan GeneMark

4 Genescan GENESCAN Length of Genes (bp) BLASTNTBLASTNBLASTPDescription Gene 1482.3 No significant Results 9.3 EDK39880 hypothetical protein PGUG_03978 [Pichia guilliermondii ATCC 6260] Gene 29907e-855e-58647 bp 1e-45 XP_002306324 predicted protein [Populus trichocarpa] Gene 34898e-365e-23742 bp 1e-09 EEF27117 conserved hypothetical protein [Ricinus communis] Gene 44891e-26 2e-08853 bp1e-08 XP_002320937 predicted protein [Populus trichocarpa]

5 GeneMark GENEMARK Length of Proteins (aa) BLASTNTBLASTNBLASTPDescription Gene 1250NA 5e-11 417 bp 0.65 AAD28219 cysteine aminopeptidase; PepC [Enterococcus faecium] Gene 294NA 2e -14 340bp 0.001 ACB28472 polyprotein [Ananas comosus] Gene 385NA 2e-08 473 bp No Significant Results N/A Gene 4305NA 2e-26 647 bp 4.3 YP_001323147 lysyl-tRNA synthetase [Methanococcus vannielii SB] Gene 5113NA 4e-13 161 bp 5e-16 EEF27794 conserved hypothetical protein [Ricinus communis] Gene 6197NA 9e-23 742 bp 2e-06 ABK28031 unknown [Arabidopsis thaliana] Gene 7160NA 7e-ll 555 bp 7e-10 XP_002320939 multidrug/pheromone exporter, MDR family, ABC transporter family [Populus trichocarpa] Gene 8170NA 5e-12 661 bp 2e-07 EEF27421 conserved hypothetical protein [Ricinus communis] Gene 9231NA 2e-18 663 bp 2.4 YP_001434725 hypothetical protein Igni_0134 [Ignicoccus hospitalis KIN4/I] Gene 10521NA9e-134 872 bp 5e-148 CAA33227 unnamed protein product [Glycine max]

6 Diagram of Predicted Genes Fgenesh Genescan GeneMark Repeat

7 Overlapping Predicted Genes Fgenesh Genescan GeneMark Repeat

8 REPEATS? Plant Repeat Database IdDescriptionE value MRSiTETN00200002 gi|13516330|emb|AJ309049.1|M TR309049 Medicago truncatula CACTA type transposable element, clone 70N13, sequence 2-1 194 GRSiTETNOOT00004 gi|170080|nt4-3553 Soybean transposable element tgm1 165 MRSiTETN00200003gi|13516329|emb|AJ309048.1|M TR309048 Medicago truncatula CACTA type transposable element, clone 75I04 163

Download ppt "The Scarlet Runner Bean Genome: Contig 230613 By Eden Maloney."

Similar presentations

44 D (3 Khipu elements) 14 12 Phaseolus vulgaris B4 locus 410 Kb contig 158 kb Sub- cluster C 400 Kb 300 Kb 250 Kb 200 Kb 150 Kb 100 Kb 50 Kb 28 21 15.

44 D (3 Khipu elements) Phaseolus vulgaris B4 locus 410 Kb contig 158 kb Sub- cluster C 400 Kb 300 Kb 250 Kb 200 Kb 150 Kb 100 Kb 50 Kb
Class I-A Class II-A Class II-B Class II- Basal Class I-B Class I Class II 0.1 Arabidopsis thaliana PHO1;H2 Capsella rubella PHO1;H11 100 Thellungiella.

Class I-A Class II-A Class II-B Class II- Basal Class I-B Class I Class II 0.1 Arabidopsis thaliana PHO1;H2 Capsella rubella PHO1;H Thellungiella.
The Trihelix Transcription Factor Family Heather Hernandez.

The Trihelix Transcription Factor Family Heather Hernandez.
Scarlet Runner Bean Genome Annotation: Contig 257429.

Scarlet Runner Bean Genome Annotation: Contig
Scarlet Runner Bean Genome Sequence: Contig232576 By Elaine Chiu.

Scarlet Runner Bean Genome Sequence: Contig By Elaine Chiu.
Annotating a Scarlet Runner Bean genome fragment put together by shotgun sequencing Scarlet Runner ean Max Bachour.

Annotating a Scarlet Runner Bean genome fragment put together by shotgun sequencing Scarlet Runner ean Max Bachour.
Characterization of sugar-response Arabidopsis (Arabidopsis thaliana) mutants to engineer plants for higher ethanol, soydiesel and soy protein production.

Characterization of sugar-response Arabidopsis (Arabidopsis thaliana) mutants to engineer plants for higher ethanol, soydiesel and soy protein production.
Max BachourJessica Chen. Shotgun or 454 sequencing High throughput sequencing technique that can collect a large amount of data at a fast rate. Works.

Max BachourJessica Chen. Shotgun or 454 sequencing High throughput sequencing technique that can collect a large amount of data at a fast rate. Works.
Topic 7 Nucleic Acids and Proteins. DNA Structure.

Topic 7 Nucleic Acids and Proteins. DNA Structure.
Scarlet Runner Bean Genome Assembly Nancy Phang June 4, 2004.

Scarlet Runner Bean Genome Assembly Nancy Phang June 4, 2004.
Genes. Outline  Genes: definitions  Molecular genetics - methodology  Genome Content  Molecular structure of mRNA-coding genes  Genetics  Gene regulation.

Genes. Outline  Genes: definitions  Molecular genetics - methodology  Genome Content  Molecular structure of mRNA-coding genes  Genetics  Gene regulation.
An Analysis of “Gene Finding in Novel Genomes” Michael Sneddon.

An Analysis of “Gene Finding in Novel Genomes” Michael Sneddon.
Many genes have unknown function 30% have unknown function only 9% are experimentally verified The Arabidopsis Genome Initiative, Nature 2000 of the 25,498.

Many genes have unknown function 30% have unknown function only 9% are experimentally verified The Arabidopsis Genome Initiative, Nature 2000 of the 25,498.
Goals of the Human Genome Project determine the entire sequence of human DNA identify all the genes in human DNA store this information in databases improve.

Goals of the Human Genome Project determine the entire sequence of human DNA identify all the genes in human DNA store this information in databases improve.
Human Genome Project Seminal achievement. Scientific milestone. Scientific implications. Social implications.

Human Genome Project Seminal achievement. Scientific milestone. Scientific implications. Social implications.
Lim et al, Supplemental Figure S1. 01.55.07.0105010015020030040050000 Arsenic Plant height (Cm) As[μM] b/c g f e d c/d a/b a c/d a a/b Cadmium 01.55.07.0105010015020030040050000.

Lim et al, Supplemental Figure S Arsenic Plant height (Cm) As[μM] b/c g f e d c/d a/b a c/d a a/b Cadmium
Arabidopsis Gene Project GK-12 April Workshop Karolyn Giang and Dr. Mulligan.

Arabidopsis Gene Project GK-12 April Workshop Karolyn Giang and Dr. Mulligan.
Figure S1: Sequence of the mtr-miR159b backbone for amiRNA expression in pBluescriptII SK+ vector. AmiRNA constructs are generated from this template using.

Figure S1: Sequence of the mtr-miR159b backbone for amiRNA expression in pBluescriptII SK+ vector. AmiRNA constructs are generated from this template using.
Genome projects and model organisms Level 3 Molecular Evolution and Bioinformatics Jim Provan.

Genome projects and model organisms Level 3 Molecular Evolution and Bioinformatics Jim Provan.
Bikash Shakya Emma Lang Jorge Diaz.  BLASTx entire sequence against 9 plant genomes. RepeatMasker  55.47% repetitive sequences  82.5% retroelements.

Bikash Shakya Emma Lang Jorge Diaz.  BLASTx entire sequence against 9 plant genomes. RepeatMasker  55.47% repetitive sequences  82.5% retroelements.

Similar presentations

Ads by Google