Cosmoss workshop

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Image:Cosmoss logo.png

This site provides online material for the www.cosmoss.org 3rd Physcomitrella Genome Workshop that will be held

on
September 13th-15th 2010
at
University of Freiburg, Germany

Last year

Contents

Sponsors


Organization is in cooperation with Kongress & Kommunikation GmbH, http://www.kongress-und-kommunikation.de

Information

Cosmoss accounts

You have to be a registered cosmoss user in order to access some of linked material.

For the workshop participants, accounts have been created (unless you already had one) with an initial password handed out at the registration desk. Please change it as soon you log in.

Everyone else is also invited to register! Please contact helpdesk-cosmoss@uhura.biologie.uni-freiburg.de for an account!

Registration

  • Deadline for registration: August 29, 2010.
  • Registration fee: 200€

Program

Learn how to work with cosmoss.org and the Physcomitrella patens genome. Find and annotate your gene(s) of interest. Get in touch with other people working with Physcomitrella and other bryophytes.

Covered topics

Tutorial sessions for the computational tools and databases available on cosmoss.org. E.g.:

  • BLAST
  • Sequence Retrieval
  • Genome Browser
  • Functional Annotation Interface genonaut
  • Structural Annotation Interface Apollo

Annotation jamboree:

  • Invited Speakers on gene annotation (see below)
  • Functional and structural annotation Howto
  • Hands-on annotation session (annotate your genes of interest)

Schedule

Monday September 13
09:00
13:00

Registration

09:30
13:15

Morning session including lunch

09:30

Welcome

09:30
10:00

The Physcomitrella Genome

10:00
10:30

cosmoss.org: resources, databases and versions

10:30
13:15

Welcome reception, industry exhibits and lab tours

13:30
17:30

Afternoon session including coffee break

13:30
14:00

Lecture: Homology searching / BLAST

14:00
14:50

Hands-on: BLAST

14:50
15:15

Lecture: gene families

15:15
15:30

Coffee break

15:30
16:00

Hands-on: gene family tools

16:00
16:40

Lecture: sequence retrieval

16:40
17:15

Hands-on: sequence retrieval/keyword search

17:30
?

Social event: Bus trip to a typical south German locality (Strauße) including evening meal


Tuesday September 14
09:00
12:00

Morning session including coffee break

09:00
10:00

Lecture:Genome browser and Hands-on: genome browser basics

10:00
10:15

Lecture: Genome Browser Tracks

10:15
10:30

Coffee break

10:30
11:00

Lecture: Genome Browser hidden treasures

11:00
12:00

Hands-on: Advanced gbrowsing & Questions

12:00
13:30

Poster session & Lunch

13:30
17:30

Afternoon session including coffee break

13:30
14:00

Lecture: functional annotation

14:00
15:00

Hands-on: genonaut

15:15
15:30

coffee break

15:30
16:00

Lecture: structural annotation (Gbrowse)/Apollo annotation editor

16:00
17:00

Hands-on: structural annotation

17:30
?

Social event: Conference dinner and industry night with talks on Physcomitrella/genome-specific applications

18:00
18:20

BMG

18:20
18:40

Agrisera

18:40
19:00

Genxpro

19:00
19:20

High-throughput transcriptomics in Physcomitrella

19:20
?

Dinner


Wednesday September 15
09:00
12:00

Morning session including coffee break

09:00
09:30

Annotating MADS-box Genes and KNOX Genes in the Physcomitrella Genome

09:30
10:00

Gene Annotation in Transcriptomic Analysis

10:15
10:30

Coffee break

10:30
12:00

Annotation guidelines, Evidence Codes, examples (Student Annotation Project) and discussion

12:00
13:30

Poster session & Lunch

13:30
17:00

Afternoon session (Annotation Jamboree) including coffee break

13:30
15:15

Gene family assignment (publications) / Jamboree

15:15
15:30

Coffee break

15:15
16:30

Jamboree

16:30
17:00

Concluding remarks / discussion

Poster session

Carolin Aldinger
Examination of the annotated tRNAArg GCG in Physcomitrella patens
Alexandra Castro
Differentially expressed genes in response to pathogens in Physcomitrella patens cancelled
Mahmoud Madgy
The genetic structure of the Funaria hygrometrica populations in Sierra Nevada (Spain) using the sequence-related amplified polymorphism (SRAP) technique
Bernadeta Kukuczka
Characterization of iron-deficiency responses and targeted knockout of the pgrl1 gene in Physcomitrella patens
James LLyod
Can moss read nonsense? Exploring gene regulation by nonsense-mediated decay in Physcomitrella
Stefanie Müller
Mitochondrial proteomics in the moss Physcomitrella patens: Are there two subpopulations of mitochondria?
Sergio Pisa
Genetic diversity of Bryum argenteum Hedw. along an altitudinal gradient in Sierra Nevada, Spain
Cecilia Ruibal
Search for genes involved in abiotic stress tolerance in Physcomitrella patens cancelled

Venue

University of Freiburg, Germany

Biology I

  • Campus, Hauptstr. 1, Computer Pool & Lounge
  • main workshop location

Google map of the location

Biology II

  • Campus, Schänzlestr. 1, Main Entrance, Small Lecture Hall & Lecture Hall Foyer
  • morning session on the first day
  • the registration desk is located in the Lecture Hall Foyer

Google map of the location

Speakers

Workshop Content

First Day

Morning Session

location
Biology II Small Lecture Hall

The Physcomitrella Genome

speaker
Stefan
slides
Genome.pptx

cosmoss.org: resources, databases and versions

speaker
Daniel
slides
cosmoss_resources_databases_versions.pdf

Afternoon Session

location
Biology I Computer Lab

Lecture: Homology searching / BLAST

speaker
Stefan
slides
BLAST.pptx

Hands-on: BLAST

speaker
Stefan
slides
BLAST_hands-on.pptx

Lecture: gene families

speaker
Stefan
slides
GeneFamilies.pptx

Hands-on: gene family tools

speaker
Stefan
slides
GeneFamiliesHands-On.pptx

Lecture: sequence retrieval and genome browser

speaker
Andreas
slides
Sequence_Retrieval_2010.pptx

Hands-on: sequence retrieval/keyword search

speaker
Andreas
Sequence Retrieval
documentation
Sequence Retrieval

Familiarize yourself with the Cosmoss Retrieval system:

Tasks

Try to retrieve the following sequences:

Pp1s1_770V6.1
Pp1s1_128V6.2
Phypa_430365


You can access the sequence retrieval via the transcriptome and genome menu.

Hint: These accession numbers above are from the annotated V1.6 P.patens transcripts database. You can retrieve multiple sequences by providing their accession numbers as a comma- or space-separated


Have a look at the receiving FASTA files.

What are the first five bases of Phypa_430365 transcript sequence? *mark text from here -->  ACTAT<-- to here for the answer*
What is the description of Pp1s1_128V6.2 ? *mark text from here --> patatin t5<-- to here for the answer*
What is the CGI (cosmoss gene id) of  Phypa_430365 ? *mark text from here --> Pp1s33_278V6.1<-- to here for the answer*

As you may have already noticed, you could retrieve your P.patens sequence (V1.1, V1.2, V1.6) of interest using the Phypa_id or CGI. e.g. Phypa_430390 or Pp1s33_43V6.1

Batch retrieval

For a vast number of sequences you could upload your request in a text file.

File format: text
Provide accession number per line.

Select the following accession numbers and copy them into a new text file (e.g. notepad) and save it.

Pp1s459_1V2.1
Pp1s7_181V2.1
Pp1s204_88V2.1
Pp1s204_91V2.1
Pp1s352_13V2.1
Pp1s312_46V2.1
Pp1s56_169V2.1
Phypa_125839
Pp1s56_166V2.1
Phypa_125903
Pp1s188_40V2.1
Pp1s545_4V2.2
Pp1s109_143V2.1
Pp1s352_57V2.1
Pp1s66_46V2.1
Pp1s12_223V2.1
Pp1s46_41V2.1
Phypa_146969
Phypa_87740
Phypa_87752
Phypa_151552
Phypa_8310
estExt_fgenesh1_pg.C_330027
EDQ76486
XM_001758564

Goto the cosmoss.org sequence retrieval:

Select database: P.patens_all_models_transcripts

This all models database contains all P.patens gene predictions (V1.0 V1.1 V1.2 V1.6) proteins.

The Physcomitrella patens genome accession numbers work for both transcripts and proteins databases. Just change the database to change to your favored sequence type.

Browse for the previously created file and submit your request

Save the sequences in a new file in FASTA format

Select only a subset of the sequences and save it to a new file

Keyword search
documentation
Keyword search

How many geranyl geranyl pyrophosphate synth(et)ases (GGPS) are in the virtual transcriptome?

Try to find the corresponding pp0304 virtual transcripts by keyword search!

Tasks
  1. Read the documentation
  2. Use the simple search menu to find the GGPS's in pp0304
  3. Play around with the advanced search option.
  4. How many geranyl geranyl pyrophosphate synthase hits to you find with the keyword search in the V1.6 transcripts?


Hits in pp0304

*mark text from here --> 3 Hits in the pp0304 transcripts <-- to here for a possible query* 

Hits in V1.6 transcripts

*mark text from here -->  5 Hits on 4 loci<-- to here for a possible query* 


This is the advanced query that works:

*mark text from here --> "geranyl geranyl"[DESC] AND "phosphate"[DESC] AND "synth"[DESC] <-- to here for a possible query* 

Finally, here are the four loci in the genome:

Second Day

Morning Session

Lecture: Genome Browser Basics

speaker
Andreas
slides
Zimmer_GenomeBrowser_10.pptx

Hands-on: Genome Browser Basics

speaker
Andreas
slides
Hands_on_gbrowse_basics.pptx

Lecture: Genome Browser hidden treasures

speaker
Daniel
slides
cosmoss_gbrowse_treasures.pdf
Hands-on experience

Genome browser: customization and special features

prepared by
Daniel
BLAST gbrowse integration
documentation
BLAST_gbrowse_integration
Tasks
  1. BLAST with an arbitrary transcript/EST vs the scaffolds and follow the Image:BLAST2gbrowse.png link.
  2. Compare results when BLASTing w/o low complexity filtering!
  3. Compare the BLAST to the spliced-alignment results. Are there lonely exons?
  4. BLAST with the Arabidopsis protein AT5G13930.1 vs the v1.2 gene models and follow the Image:BLAST2gbrowse.png link.
  5. Compare one of the hit Physcomitrella loci vs the Arabidopsis locus AT5G13930
Advanced navigation and zooming
Tasks
  1. Find out the definition of a gene in SO by using the Ontology_term cross-link in a gene feature's mouse-over window
  2. Zoom into a CDS exon and back again to the region of its mommy mRNA or gene
  3. Play around with the zoom function to inspect EST and cDNA spliced alignments!
Exporting sequence annotations and publication quality images
Tasks
  1. Export the upstream 10kbp your most favorite region to FASTA format and reverse it when necessary to reflect the gene's orientation.
  2. OPTIONAL: Get another upstream region and try to find shared putative promoter elements using e.g. AlignACE
  3. Save your most favorite region as a png image.
  4. Check out the exemplary PDF created with Inkscape from the SVG of a region: www.cosmoss.org.inkscape_example.pdf
Highlighting
example locus
scaffold_29:573541..579040
documentation
available colors (scroll down to Colors)
Tasks
  1. Let gbrowse highlight a feature and zoom out again, in order to see whether it overlaps with another feature in another track (highlight and zoom to the region of this feature link in the mouse-over)
  2. Highlight your favorite gene model for the locus using the Highlight feature box in the Display panel.
  3. Visualize an PCR experiment on the genomic locus! You've just amplified and sequenced an genomic PCR product for the locus using the primer coordinates below. Highlight the genomic region using the Highlight regions box in the Display panel.
forward primer mapping
scaffold_29:575397..575417
reverse primer mapping
scaffold_29:577964..577950

Image:Cosmoss_workshop_gbrowse_treasures_highlight.png

Displaying custom annotation

You can draw your own features and have your own custom track in the browser!

documentation
gbrowse custom annotation help
example locus
scaffold_29:573541..579040
Tasks
  1. Go through the documentation
  2. Visualize an RT-PCR experiment on the genomic locus! You've just amplified and sequenced an RT-PCR product for the locus below. Display it as custom annotation using the coordinates:
RT-exon1 scaffold_29:575397..575570
RT-exon1 scaffold_29:576849..576875
RT-exon1 scaffold_29:577042..577335
RT-exon1 scaffold_29:577629..577692

See the example file which combines everything. Adjust it, if you like!

Lecture: functional annotation

speaker
Daniel
slides
cosmoss_genonaut.pdf

Live presentation: Upcoming structural annotation at cosmoss.org using gbrowse and Apollo

speaker
Daniel

Third Day

Morning Session

Invited talk: Annotating MADS-box Genes and KNOX Genes in the Physcomitrella Genome

speaker
Elizabeth Barker
abstract
Talk.Elizabeth_Barker.abstract.pdf
slides
Barker_Cosmoss_Workshop_2010.ppt

Invited talk: Gene Annotation in Transcriptomic Analysis

speaker
Andrew Cuming
abstract
Talk.Andrew.Cuming.abstract.pdf
slides
Cuming_Freiburg_2010.ppt

Lecture: Annotation Guidelines, Student Annotation Project and Moss Ontology

speaker
Daniel
slides
Annotation.pdf

Lecture: Annotation examples

speaker
Stefan
slides
AnnotationExamples.pptx
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