JBrowse HowTo

·       Select strain

·       Search

·       Download

·       Navigation

·       Views

·       Sharing & Marking

·       Data Sources

·       Homologs

·       Software Sources



The genome browser contains 3 P. pastoris genomes:

·       Komagataelle phaffii CBS7435

·       Komagataella phaffii GS115

·       Komagatella pastoris DSMZ 70382

And 1 Saccharomyces cerevisea genome SC 288C.

For every genome different data tracks, containing diverse information, are available. You can select the tracks on the menu on the left side.

How to display/select a strain or species in the Stand-Alone JBrowse

Click „Genome“ in the top menuselect the desired strain or species. The left menu will change according the available information for the strain or species.


How To Search for a feature

There are several options to search for features like genes etc.

1.       Enter the combination of chromosome/contig/scaffold plus the region range you want to view. Example: cbs7435:0..100
It is also possible to select the contig/chromosome/scaffold from the drop down menu on the left side of the textbox you can see on the right side.

2.       Enter the gene name of the feature you are looking for into the textbox. While typing you will see matching suggstions. You can also type in the feature name.
Select the match from the drop down list and click „Go“. A new PopUp window will open. There you can choose between „Show“ and „Go“ for the found features matching your searchterm. „Go  will bring you directly to the chosen feature and close the pop up, „Show“ will do the same while leaving the pop up open.



How to Retrieve/Download Sequences

1.       In „View Details“
Right Mouse Click on the feature you want the sequence for. Choose „View Details“ – a window opens containing one or more versions of the feature sequence where you can do a copy and paste. If there is no context menu „View Details“ by right clicking a track, you can do a simple left mouse click on the feature to open the details window.

2.       In GFF-, BED-, Sequin-Format
Open the context menu of some track – not reference sequence track - and choose „Save track data“. You have the option to save the sequence in the three formats. Also you can choose if you want to save only the visible region or the complete reference sequence.

3.       Whole Reference Genome
See the paragraph above.

4.       Nothing above
If you need a chunk of sequence which is not part of a feature-track, you can fetch it by utilizing the reference sequence. Zoom into the exact section you need, then select the reference sequence track on the left menu. Now you can download thesequence in fasta format by clicking the drop down menu, choose "Save track data" and clicking "View" or "Save"









How to navigate in JBrowse

1.       Zoom in and out
- Double Click multiple times at the position you want to zoom in
- Magnifier button: Press +/- on the magnifier buttons
- Drag & Drop the coursor either on the upper or the lower  coordinate ruler    

2.       Moving left/right
- Click the arrows to the left or right
- Drag & Drop the page at empty position with the coursor

3.       Hiding track menu to prevent it overlapping data, use the „Hide“-Button




1.       Different Tracks have a different appearance depending on the type of data and the zoom status

2.       A details view can be reached by right clicking on the track, apart from the „mRNA + SeqLighter“ Tracks. In the „mRNA + SeqLighter“ just use the left mouse button instead.

3.       In the „mRNA + SeqLightertrack you can reach the SeqLighter-Plugin via the right-click context menuchoose „View Sequence“. Beside the possibility to download the sequence in different formats you can choose some ranges on flanking regions tob e displayed and downloaded as well.


Sharing and Marking information

You can send a link to the current view you are looking at using the „Share“-Button on the right upper corner.

You can mark a region using the highlighter-button next to the search textbox

Data Sources

1.       Pichia pastoris CBS7435
The CBS7435 strain was sequenced by the Institute for Genomics and Bioinformatics, Graz University of Technology (Austria).
Reference: High-quality genome sequence of Pichia pastoris CBS7435, Journal of Biotechnology 2011, 154(4):312-20
The hosted sequence version is from 27-FEB-2015 (NCBI)

The annotation was curated 2016. This data is part of this database and genome browser.
Reference: Valli et.al.,Curation of the genome annotation of Pichia pastoris (Komagataella phaffii) CBS7435 from gene level to protein function

2.       Pichia pastoris GS115
The GS115 strain was sequenced by the VIB Ghent, Department of Biomedical Molecular Biology.
Reference: De Schutter et al.,Genome sequence of the recombinant protein production host Pichia pastoris, Nature Biotechnology 27, 561 - 566 (2009)
The hosted sequence version is from 27-FEB-2015 (NCBI)

3.       Pichia pastoris DSMZ70382
The DSMZ 70382 strain was sequenced by the University of Natural Resources and Applied Life Sciences, Vienna, Department of Applied Microbiology.
Reference: Mattanovich et al., Genome, secretome and glucose transport highlight unique features of the protein production host Pichia pastoris, Microbial Cell Factories 2009, 8:29

4.       Saccharomyces cerevisiae S288c
The sequenceinformation of S.cerevisiae S288c was downloaded from yeastgenome.org (genome, Coding Sequences) on February, 10th 2016

Homologs in other Strains & Species

The homologs were derived from a simple BLAT run of the according coding sequences (CDS) against a genomic sequence (all in nucleotide sequences). Blast was chosen as output format, so that a previously used Blast parser could be used to determine the hits.

Example call:

blat cbs7435_genomic.fasta sc_orf_coding_all.fasta -t=dna -q=dna -out=blast sc_cds_vs_cbs7435.blast

The result was parsed the way, that only the best HSPs got into the output. The used cut offs were:

·       Fraction conserved aka fraction similar of 0.4

·       Length of 50

Software Sources

1.       JBrowse

2.       SeqLighter: A plugin developed by Maria Kim and Vivek Krishnakumar for the Araport Website (URL)


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