Monday, 31 August 2015

The SMRT way to sequence a yeast genome

Rich will be giving this week’s BABS School seminar (as part of a double header),

The SMRT way to sequence a yeast:
de novo genome sequencing and assembly with PacBio

Rountree Room Level 3
D26 Biological Sciences Building, UNSW
Friday 4 Sept 3.00pm


We have performed PacBio single molecule real time (SMRT) sequencing of three yeast whole genomes. A haploid reference yeast strain (S288C) and two novel diploid strains were sequenced as part of a larger functional genomics project. For each strain, 2-2.6 Gb of usable sequence data was generated with read lengths of up to 53.3 kb. Pure PacBio whole genome de novo assemblies were generated using the HGAP3 pipeline. initial assembly of S288C yielded over 99.9% genome coverage at 99.997% accuracy with 15 of 17 reference chromosomes (16 nuclear chromosomes plus mitochondrion) essentially returned as a single, complete unitig. We are now using the S288C data to optimise the assembly process and derive assembly settings for the two novel strains. To this end, we have developed a new pipeline for the comparative assessment of high quality whole genomes against a reference. We are also exploring the trade-off between accuracy and sequencing depth of the PacBio “pre-assembly” and how this affects the final assembly.

[This work will also be presented at AGTA 2015, if you are interested and miss it.]

Friday, 7 August 2015

SLiMScape 3.x: a Cytoscape 3 app for discovery of Short Linear Motifs in protein interaction networks

The latest paper from the lab (featuring work from Emily Olirin’s summer project) is now out at F1000Research. We’ve not gone down the post-publication peer review route before, so it will be interesting to see how that goes, but it made sense in this case as it’s part of a special Cytoscape Apps channel. Rest assured that it has undergone technical review, just not scientific review. [At time of submission: peer review now complete.]

Olorin E, O’Brien KT, Palopoli N, Pérez-Bercoff A, Shields DC, Edwards RJ (2015): SLiMScape 3.x: a Cytoscape 3 app for discovery of Short Linear Motifs in protein interaction networks [version 1; referees: 2 approved]. F1000Research 4:477. (doi: 10.12688/f1000research.6773.1)


Short linear motifs (SLiMs) are small protein sequence patterns that mediate a large number of critical protein-protein interactions, involved in processes such as complex formation, signal transduction, localisation and stabilisation. SLiMs show rapid evolutionary dynamics and are frequently the targets of molecular mimicry by pathogens. Identifying enriched sequence patterns due to convergent evolution in non-homologous proteins has proven to be a successful strategy for computational SLiM prediction. Tools of the SLiMSuite package use this strategy, using a statistical model to identify SLiM enrichment based on the evolutionary relationships, amino acid composition and predicted disorder of the input proteins. The quality of input data is critical for successful SLiM prediction. Cytoscape provides a user-friendly, interactive environment to explore interaction networks and select proteins based on common features, such as shared interaction partners. SLiMScape embeds tools of the SLiMSuite package for de novo SLiM discovery (SLiMFinder and QSLiMFinder) and identifying occurrences/enrichment of known SLiMs (SLiMProb) within this interactive framework. SLiMScape makes it easier to (1) generate high quality hypothesis-driven datasets for these tools, and (2) visualise predicted SLiM occurrences within the context of the network. To generate new predictions, users can select nodes from a protein network or provide a set of Uniprot identifiers. SLiMProb also requires additional query motif input. Jobs are then run remotely on the SLiMSuite server ( for subsequent retrieval and visualisation. SLiMScape can also be used to retrieve and visualise results from jobs run directly on the server. SLiMScape and SLiMSuite are open source and freely available via GitHub under GNU licenses.

Monday, 3 August 2015

ABACBS 2015: Register now!

ABACBS 2015, the national conference for bioinformatics, will be held in Sydney this year. Registration and abstract submissions are now open! Closing date for abstract submissions is the 14th of August.

If the low cost isn’t enough incentive, there will be prizes for best poster, fast forward poster presentation and oral presentation…

Date: 10-11 October 2015 (preceding AGTA 2015) Venue: Garvan Institute of Medical Research, Sydney Cost: $99 (or $124 including a BBQ Dinner).

More details (and registration links):

Questions? Email us:

Additional events in Sydney this year:

COMBINE student symposium Oct 9, registration now open: BioInfoSummer Dec 7-11 at the University of Sydney: