HFSP: high speed homology-driven function annotation of proteins Yannick Mahlich, Martin Steinegger, Burkhard Rost, Yana Bromberg
Bioinformatics, Volume 34, Issue 13, 1 July 2018, Pages i304–i312 https://doi.org/10.1093/bioinformatics/bty262
The rapid drop in sequencing costs has produced many more (predicted) protein sequences than can feasibly be functionally annotated with wet-lab experiments. Thus, many computational methods have been developed for this purpose. Most of these methods employ homology-based inference, approximated via sequence alignments, to transfer functional annotations between proteins.
mi-faser: major update of web-service and standalone-version New in the public web-service:
NMDS analysis between submitted samples
Register user account for faster access to submissions / analyses
faster submission processing (less then ~15min per 20GB reads)
Batch submissions (up to 100 input files)
Paired-end input processing
Quality-Control pipeline for fastq input
New in the standalone-version:
threaded processing (split input files and process in parallel)
built-in up/downgrade to diamond version of choice
Functional sequencing read annotation for high precision microbiome analysis Chengsheng Zhu, Maximilian Miller, Srinayani Marpaka, Pavel Vaysberg, Malte C. Rühlemann, Guojun Wu Femke-Anouska Heinsen, Marie Tempel, Liping Zhao, Wolfgang Lieb Andre Franke, Yana Bromberg. Nucleic Acids Research, https://doi.org/10.1093/nar/gkx1209
The mi-faser microbiome analysis pipeline, combining faser with our manually curated reference database of protein functions, accurately annotates microbiome molecular functionality. mi-faser’s minutes-per-microbiome processing speed is significantly faster than that of other methods, allowing for large scale comparisons.
Dr. Yana Bromberg is chairing the Proteins session of the fourth International Society for Computational Biology Latin America Bioinformatics Conference (ISCB-LA) together with Dr. Diego U. Ferreiro (Laboratorio de Fisiología de Proteins, Dpto Química Biológica / IQUIBICEN-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires).
fusionDB: assessing microbial diversity and environmental preferences via functional similarity networks Zhu Chengsheng, Mahlich Yannick, Miller Maximilian, Bromberg Yana; fusionDB: assessing microbial diversity and environmental preferences via functional similarity networks, Nucleic Acids Research, https://doi.org/10.1093/nar/gkx1060
We describe fusionDB, a novel database that uses our functional data to represent 1374 taxonomically distinct bacteria annotated with available metadata: habitat/niche, preferred temperature, and oxygen use. Each microbe is encoded as a set of functions represented by its proteome and individual microbes are connected via common functions.
We developed clubber (CLUster-load Balancer for Bioinformatics E-Resources) to automate distribution of computation between independent and heterogenous compute resources based on individual workloads, queueing, and computation times.
clubber is available as docker image and as GitHub repository via bitbucket.
Publication: JIB, https://doi.org/10.1515/jib-2017-0020
Dr. Yana Bromberg spoke at the virtual conference Genetics and Genomics 2017. The title of the talk is: “What went wrong in the prediction of functional effects of exomic variation”.
The talk is available on YouTube.
A paper came out in Nature Scientific Reports with collaborators Jonas Reeb, Maximilian Hecht, Maria Schelling, Tjaart Andries Petrus De Beer, Yana Bromberg & Burkhard Rost.
The title of the paper is “Common sequence variants affect molecular function more than rare variants?”
On May 10th Dr. Yana Bromberg gave an invited talk at the invitation of Dr. Liping Zhao at Shanghai Jiao Tong University in Shanghai, China.
The title of the talk is “Functional basis of microbiome annotation: theory to practice”.