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

Themenübersicht der Vorlesungen

VLDatumRaumUhrzeitThema
VL 0109.10.17 R 109 10:15
VL 0216.10.17 R 109 10:15
VL 0323.10.17 R 109 10:15
VL 0430.10.17 R 109 10:15
VL 0506.11.17 R 109 10:15
VL 0613.11.17 R 109 10:15
VL 0720.11.17 R 109 10:15
VL 0827.11.17 R 109 10:15
VL 0911.12.17 R 109 10:15
VL 1018.12.17 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

tutorial notes from Alex (PDF) (updated Jan. 14, 2018)

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 IDorganism with query proteinrecipient lineagedonor lineage
1EDQ83581Physcomitrella patensplantfungi
2EDQ61440Physcomitrella patensfungi plant
3EAU93280Coprinopsis cinereaplantfungi
4XP_389330Fusarium graminearumplantfungi
5EDR08700Laccaria bicolorplantfungi
6EDQ68642Physcomitrella patensplantfungi
7EDR02747Laccaria bicolorfungi plant
8ABK92591Populus trichocarpafungi plant
9EDN23584Botryotinia fuckelianafungi plant
10XP_002380973.1Aspergillus flavus fungibacteria
11XP 006844603.1 Amborella trichopoda plantbacteria
12XP 008716975.1 Cyphellophora europaea fungibacteria
13XP 001824994.1 Aspergillus oryzae fungibacteria
14KFY76848.1 Pseudogymnoascus pannorum fungibacteria
15KGN48246.1 Cucumis sativus plantfungi
16XP 002537299.1 Ricinus communis plantbacteria

Gene-Category-B collection (No-one knows if HGT has occurred):

#files/info
1 and 9EnsemblID: ENSG00000166743, link to protein on NCBI web site
2 and 10files to download
3 and 11files to download
4 and 12files to download
5 and 13files to download
6 and 14files to download
7 and 15files to download
8 and 16files to download

Seminar

Linux onna stick iso

Youtube-tutorials fuer den Linux terminal (Sinnvoll fuer Anfaenger und Insomniageplagte)

Sinnvoll sind auch sogenannte "Cheat sheets"

Im internet nach alternativen suchen

Literatur

ClustalW
Muscle
T-Coffee
Boeckenhauer und Bongartz: Algorithmische Grundlagen der Bioinformatik; Teubner, Wiesbaden; ISBN 3-519-00398-8
Durbin, Eddy, Krogh and Mitchison: Biological Sequence Analysis; Cambridge University Press; ISBN 0-521-62971-3
Wuenschiers: Wiley Schnellkurs Bioinformatik fuer Anwender; Wiley-VCH; ISBN: 978-3-527-53040-3