annotation update

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Annotation Update. By: Sandra, Tal, Morella. MarQuardt: A3 Phage Annotated. Genes 1-20 Tal: Genes 1-8 Morella: Genes 9-16 Sandra: Genes 17-20. Areas of Confusion. Is this genes coding potential all included?. More Areas of Confusion. - PowerPoint PPT Presentation


  • Annotation UpdateBy: Sandra, Tal, Morella

  • MarQuardt: A3 Phage AnnotatedGenes 1-20Tal: Genes 1-8Morella: Genes 9-16Sandra: Genes 17-20

  • Areas of ConfusionIs this genes coding potential all included?

  • More Areas of ConfusionIt was hard to see which gene was which between DNA Master and the Phamerator MapsGene 1 was confusing as to whether it was actually a gene or not because of all the factors that played inGene 1 was also difficult because it was the first gene annotated

  • Genes Added or DeletedNo genes were added to our annotated genesGene 1 was deleted-Lack of start codon-No Blast match-Gene is too short-Coding potential is just a peak

  • Interesting FeaturesThere are 3 tRNAs in our section to annotateWe have not annotated them yet

  • Interesting featuresGene 5 and 7 had an overlap with the previous gene, so they were both changed and their SD scores and ORFs were loweredGene 5Gene 7

  • More Interesting FeaturesFor the blast match, genes 10-16 match with Vix or Bxz2Only gene 9 matches with JHC117 in our sequence annotatedFor the blast match, genes 17-20 all matched with Bxz2

  • Phamerator Summary

    GenePhamNumber of MembersCluster26482101A1-A10, T, Muddy31843140A1-A104210453A3, A4, A7, A105377469A2-A4, A6, A7, A9, A1066505200A2-A6, A8-A10, B1-B5, F1, I1, I2, K1-K5, L1, L3, M, N, P, Dori, Muddy, Patience, Sparky-draft7210226A2-A4, A1084284423A1-A10, B1-B5, C1, D, E, F1, F2, G, H1, H2, I1, I2, J, K1-K5, L1-L3, M, N, O, P Q, R, S, T, DS6A, Moo Moo draft, Muddy, Patience, Sparky-draft, Wildcat93634347A1-A5, A7-A8, A10, B1-B4, C1, F1-F2, G, I1, J, K1-K5, L1-L3, M, N, O, P, Q, R, DS6A, MooMoo-Draft, Patience, Wildcat104144148A1-A1, S, T, DS6A, Muddy, Sparky-Draft116487151A1-A10, J, S, T, Muddy121839141A1-A1013184095A1-A1014184195A1-A101525578A2-A4, A6, A7, A9, A10167140A1-A10176504119A1-A10, B4, I1. I2, K4, N, P, Dori188140A1-A10199140A1-A102010140A1-A10

  • Gene 8 Pham CircleThis map displays that Pham 4284 is found in many different Clusters

  • Map of Patience and MarQuardt

  • Questions RemainingCoding potential of gene 16Genes 17-20 were straightforward and only a few start codons were changedThe 3 tRNAs need to be annotated

    **We annotated genes 1-20 on MarQuardt, which is an A3 phage.*We are not sure if gene 16's coding potential is all included, which is shown by the pointing arrow. What do you think?***Gene 1 was deleted because it didnt have a start codon, there was no Blast match, the gene was too short, and there wasnt much coding potential.*There are no start codons in gene 1's sequence as shown above, which is one of the reasons why we decided to delete it.*The three tRNAs are shown above in the picture as blue rectangles, which the arrow is pointing at.*The ORFs shown in the picture are the changed versions of genes 5 and 7, which shows that there is a slight gap between each gene with the previous gene. The ORFs shown are highlighted green. Genes 5 and 7 are the green bars on the right side, which the arrows are pointing at. The ORFs can't be any longer because there would be too much overlap with the previous gene.*The blast matches were all 1:1 for the genes listed above.*This chart displays for each gene the Pham, number of members in each Pham, and what clusters are in each Pham. Pham is short for Phamily. For the genes we annotated, twelve Phams are unique to Cluster A. None of our genes are unique to only Cluster A3. The other Clusters these genes in MarQuardt share Phams with are listed in the table above.The members of this Pham are in Clusters A1-A10, B1-B5, C1, D, E, F1, F2, G, H1, H2, I1, I2, J, K1-K5, L1-L3, M, N, O, P Q, R, S, T, DS6A, MooMoo draft, Muddy, Patience, Sparky-draft, Wildcat, which is shown by all the lines in the Pham circle.*The top half of the maps are Patience and the bottom half of the maps are MarQuardt. Patience and MarQuardt have two genes in common, one in the Pham 4284 (big circles) and another in the Pham 3634 (small circles). The map is all white because the genes are too far apart. We used the Hoverlight circles and moved the map of MarQuardt but still, there is no purple. It might be due to the fact that Patience is a singleton. **The coding potential of gene 16 was discussed in an earlier slide. The few start codons that were changed were a better fit than the previously called start codons.