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Genome properties in 2019: a new companion database to InterPro for the inference of complete functional attributes

Lorna J Richardson, Neil D Rawlings, Gustavo A Salazar, Alexandre Almeida, David R Haft, Gregory Ducq, Granger G Sutton, Robert D Finn
2018 Nucleic Acids Research  
To increase the scope of coverage, we have migrated GPs to function as a companion resource utilizing InterPro entries.  ...  Genome Properties (GPs) define such functional entities as a series of steps, originally described by either TIGRFAMs or Pfam entries.  ...  ACKNOWLEDGEMENTS The authors gratefully acknowledge Peter Karp for help and support with the incorporation of MetaCyc data into Genome Properties. FUNDING  ... 
doi:10.1093/nar/gky1013 pmid:30364992 fatcat:cfganwexh5b5dhq53n2xzypxv4

Evolution of Protein Domain Architectures [chapter]

Sofia K. Forslund, Mateusz Kaduk, Erik L. L. Sonnhammer
2019 Msphere  
Genome evolution models that have been suggested to explain the shape of these distributions are reviewed, as well as evidence for selective pressure to expand certain domain families more than others.  ...  We end by a discussion of some available tools for computational analysis or exploitation of protein domain architectures and their evolution.  ...  Under these stringent cutoffs for considering a domain to be present in a kingdom, 140 domains, 15% of the CATH families found in at least one prokaryote genome, were inferred to be ancient.  ... 
doi:10.1007/978-1-4939-9074-0_15 pmid:31278674 fatcat:ar4kamphfzcn7hcdidvi7z4rgq

Accessing Cryptosporidium Omic and Isolate Data via [chapter]

Susanne Warrenfeltz, On Behalf of the EuPathDB Team, Jessica C. Kissinger
2019 Msphere  
These resources are freely available, are web-based, and permit users to analyze their own sequence data in the context of reference genome sequences in our user workspaces.  ...  CryptoDB ( ) was launched in 2004 following the appearance of draft genome sequences for both C. parvum and C. hominis.  ...  It is important to bear in mind the relative completeness of each of the sequences when searching the database.  ... 
doi:10.1007/978-1-4939-9748-0_10 pmid:31452162 fatcat:p7auusbbsnfedfcuf3udpp4iwq

Integrative computational microbial genomics for large-scale metagenomic analyses

Francesco Beghini
In only a few years, these methods have evolved so far as to ease a more precise community profiling and to allow high-level strain resolution.  ...  With an almost exponential increase in the number of reference genomes deposited daily in public data sets, current computational methods are incapable of managing and exploiting such a rich reference  ...  As a companion paper of sharing the same data, in this work, I performed the 16S rRNA analysis with QIIME and contributed to the creation of the R package for future reproducibility of the sztudy through  ... 
doi:10.15168/11572_296396 fatcat:dzdsnnuhdbgbjcmwyejvuxuo4e

Diagnostics development for the neglected parasitic diseases strongyloidiasis and visceral leishmaniasis

T Marlais
There is a need for diagnostic tests that are rapid, simple to use and deployable in field conditions to diagnose infection and validate cure.  ...  The computational method of antigen selection used here for S. stercoralis can be applied to multiple parasitic helminth infections using the wealth of open access 'omic' data.  ...  We thank Marleen Boelaert of the Institute of Tropical Medicine, Antwerp, 475 Belgium, for securing funding for the NIDIAG project, of which this work was part.  ... 
doi:10.17037/pubs.04654991 fatcat:x5dbaqqc65d5tcretcl7r6bopq

Regulation of cAMP-Dependent Gene Expression in Airway Epithelial Cells: A Transcriptional and Pharmacodynamic Analysis [article]

Dong Yan, University Of Calgary, Mark A. Giembycz
Based on these historical data, the first objective of the work reported here was to "mine" the LABA-regulated transcriptome for additional genes with disease-relevant functions.  ...  Roflumilast is a phosphodiesterase (PDE) 4 inhibitor approved by the United States Food and Drug Administration as an 'add-on' therapy for patients with severe, bronchitic COPD with a history of frequent  ...  Conclusions The results presented in this chapter implicate widespread changes in gene expression in the mechanism of action of PDE4 inhibitors in COPD especially when added on to a LABA and, by inference  ... 
doi:10.11575/prism/36795 fatcat:fdnz5z5vvnco5lgyyd3iegfniq

Exploring Early Stages of Protein Evolution

Leonhard Josef Heizinger
For a fully automated detection of putative ancestral fragments, the algorithm FragStatt was developed. It assesses proteins pairwise in order to find shared frag- ments.  ...  In contrast to the evolution of homologs that share the same fold but possess substantially different functions, the origin of the architecture of individual domains is unclear.  ...  Alignment S1: Alignment of PDB-ID 2XBL_B and PDB-ID 2YVA_A. Alignment generated using EMBOSS Needle (Madeira et al., 2019)  ... 
doi:10.5283/epub.43604 fatcat:ig6vyony4jbkdk23sywjtnctku

A Reverse Vaccinology Approach to Identifying Vaccine Candidate Antigens for Bovine Trichomoniasis

Eleanor Senior
An attempt was made to use the companion server [272] to annotate the genome. Companion uses a reference-based approach to identify genes.  ...  The relative abundances are compared to a database of known peptides and the identity of the proteins present in the sample may be inferred computationally.  ...  Mapping of the reads to the assembled and annotated T. foetus genome was performed using Hisat2 on the Galaxy Server.  ... 
doi:10.17638/03118238 fatcat:j2snavpaxvebddvexu7ixjb3wa

State-of-the-art mass spectrometry for the discovery and identification of biodiverse natural toxins [article]

Benjamin-Florian Hempel, Technische Universität Berlin, Roderich D. Süssmuth
Down to the present day, several technical improvements of analytical sciences helped to get a deeper insight to complex biological systems and understanding of the mode of action for toxigenic agents.  ...  The introduction of mass spectrometry, a major key player of analytical spectrometric instruments in mid of the 20th century, resulted in many well-funded, large-scale screening programs and gained momentum  ...  The full structure elucidation of albicidin by a combination of biochemical and analytical experiments in combination with a complete genome from X. albilineans paved the way to look for more and minor  ... 
doi:10.14279/depositonce-12282 fatcat:i7t7tmbuyjgtnpo65oax2p6sii