Sequenzanalyse und Genomik (Modul 10-202-2207)
| Vorlesung: | Raum 109, Härtelstr. 16-18; Mo 10:15-12:15 Uhr | |
| Übung: | Raum 006, Härtelstr. 16-18; Mo 17:15-19:00 Uhr | |
| Praktikum: | Raum 109, Härtelstr. 16-18 Gruppe 1: 08.01.2018 - 19.01.2018 (Mo-Fr) Gruppe 2: 22.01.2018 - 02.02.2018 (Mo-Fr) Anmeldung | |
| Prüfung | Anmeldung Ort: Haertelstr. 16-18, Raum 309 (Bibliothek Bioinformatik) |
Prüfung
Anmeldung: jeweils 3 Personen pro Termin Sollten am Ende der Registrierung Termine mit nur einer oder zwei Personen belegt sein, werden die betreffenden Personen u.U. auf einen anderen (bevorzugt spaeteren) Termine von den Veranstaltungsleitern umgebucht.Themenübersicht der Vorlesungen
| VL | Datum | Raum | Uhrzeit | Thema |
|---|---|---|---|---|
| VL 01 | 09.10.17 | R 109 | 10:15 | |
| VL 02 | 16.10.17 | R 109 | 10:15 | |
| VL 03 | 23.10.17 | R 109 | 10:15 | |
| VL 04 | 30.10.17 | R 109 | 10:15 | |
| VL 05 | 06.11.17 | R 109 | 10:15 | |
| VL 06 | 13.11.17 | R 109 | 10:15 | |
| VL 07 | 20.11.17 | R 109 | 10:15 | |
| VL 08 | 27.11.17 | R 109 | 10:15 | |
| VL 09 | 11.12.17 | R 109 | 10:15 | |
| VL 10 | 18.12.17 | R 109 | 10:15 |
Praktikum
Das Praktikum findet wie folgt statt:
| Raum: | 109, Härtelstr. 16-18 |
| Zeit: | ganztägig, Kernzeit: 10-16Uhr |
| Datum: | Gruppe1: 08.01.2018 - 19.01.2018, Gruppe2: 22.01.2018 - 02.02.2018 |
Papers to read BEFORE the Praktikum
Please read all of the following 3 papers before the Praktikum begins:- Ravenhall, et al. (2015) Inferring horizontal gene transfer, PLoS Comput. Biol., 11:e1004095. link to paper
- Soucy, et al. (2015) Horizontal gene transfer: building the web of life, Nat. Rev. Genet., 16:472-482. link to paper
- Lawrence & Ochman (1997) Amelioration of bacterial genomes: rates of change and exchange, J. Mol. Evol., 44:383-397. link to PDF
Format of presentations
Group presentation on aspects of papers read:
- Will take place start of 2nd day. (Group 1: presentations begin at 10:00 on 09.01.2018. Group 2: presentations begin at 10:00 on 23.01.2018.)
- Talks are maximum 20 minutes
- Talks must be in English
Individual presentation on analysis and results
- Will take place on last day of Praktikum. (Group 1: 19.01.2018. Group 2: 02.02.2018.)
- Your slides in PDF format are due by 13:00 on that day (by USB stick or e-mail). We will begin presentations at 14:00.
- Talks are maximum 10 minutes, plus 2 additional minutes for questions.
- Talks must be in English
handouts for Praktikum
These are handouts from the tutorial presentation by Alejandro Nabor Lozada-Chávez:
- presentation slides (PDF)
- tutorial notes (PDF)
Genes to analyze during Praktikum
You will get two genes to analyze for horizontal gene transfer (HGT), from "Category A" and "Category B". Gene-Category-A: your first gene is an example where HGT is known to have occurred. Gene-Category-B: your second gene is an example where it is not yet known whether HGT has occurred.
Gene-Category-A collection (HGT is known to have occurredp; "recipient" means the organism that received the gene via HGT and "donor" means the organism that the gene came from.):
| # | protein ID | organism with query protein | recipient lineage | donor lineage |
|---|---|---|---|---|
| 1 | EDQ83581 | Physcomitrella patens | plant | fungi |
| 2 | EDQ61440 | Physcomitrella patens | fungi | plant |
| 3 | EAU93280 | Coprinopsis cinerea | plant | fungi |
| 4 | XP_389330 | Fusarium graminearum | plant | fungi |
| 5 | EDR08700 | Laccaria bicolor | plant | fungi |
| 6 | EDQ68642 | Physcomitrella patens | plant | fungi |
| 7 | EDR02747 | Laccaria bicolor | fungi | plant |
| 8 | ABK92591 | Populus trichocarpa | fungi | plant |
| 9 | EDN23584 | Botryotinia fuckeliana | fungi | plant |
| 10 | XP_002380973.1 | Aspergillus flavus | fungi | bacteria |
| 11 | XP 006844603.1 | Amborella trichopoda | plant | bacteria |
| 12 | XP 008716975.1 | Cyphellophora europaea | fungi | bacteria |
| 13 | XP 001824994.1 | Aspergillus oryzae | fungi | bacteria |
| 14 | KFY76848.1 | Pseudogymnoascus pannorum | fungi | bacteria |
| 15 | KGN48246.1 | Cucumis sativus | plant | fungi |
| 16 | XP 002537299.1 | Ricinus communis | plant | bacteria |
Gene-Category-B collection (No-one knows if HGT has occurred):
| # | files/info |
|---|---|
| 1 | EnsemblID: ENSG00000166743, link to protein on NCBI web site |
| 2 | files to download |
| 3 | files to download |
| 4 | files to download |
| 5 | files to download |
| 6 | files to download |
| 7 | files to download |
| 8 | EnsemblID: ENSG00000047457, link to protein on NCBI web site |
| 9 | EnsemblID: ENSG00000265203, link to protein on NCBI web site |
| 10 | EnsemblID: ENSG00000181019, link to protein on NCBI web site |
| 11 | EnsemblID: ENSG00000132744, link to protein on NCBI web site |
| 12 | EnsemblID: ENSG00000170961, link to protein on NCBI web site |