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The landscape of human mutually exclusive splicing
TLDR
Evidence is provided for the expression of over 855 MXEs, 42% of which represent novel exons, increasing the annotated human mutually exclusive exome more than five-fold and offers new insights into MXE splicing mechanics and evolution.
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Waggawagga: comparative visualization of coiled-coil predictions and detection of stable single α-helices (SAH domains)
TLDR
UNLABELLED Waggawagga is a web-based tool for the comparative visualization of coiled-coil predictions and the detection of stable single α-helices (SAH domains) and a window-based score has been developed to predict SAH domains.
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Waggawagga-CLI: A command-line tool for predicting stable single α-helices (SAH-domains), and the SAH-domain distribution across eukaryotes
TLDR
Waggawagga-CLI is presented, a command-line tool for predicting and analysing SAH-domains in protein sequence datasets and allows the user to adjust the stabilizing and destabilizing contribution of amino acid interactions in i,i+3 and i, i+4 spacings, and provides extensive flexibility for user-designed analyses.
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diArk – the database for eukaryotic genome and transcriptome assemblies in 2014
TLDR
The database diArk has been developed with the aim to provide access to all available assembled genomes and transcriptomes and has also integrated species, for which transcriptome assemblies are available, and it provides more analyses of assemblies.
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Distribution and evolution of stable single α-helices (SAH domains) in myosin motor proteins
TLDR
The largest available myosin sequence dataset is analysed consisting of 7919 manually annotated myOSin sequences from 938 species representing all major eukaryotic branches using the SAH-prediction algorithm of Waggawagga, a recently developed tool for the identification ofSAH-domains.
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The Protein-Coding Human Genome: Annotating High-Hanging Fruits.
The major transcript variants of human protein-coding genes are annotated to a certain degree of accuracy combining manual curation, transcript data, and proteomics evidence. However, there is…
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Correction: Distribution and evolution of stable single α-helices (SAH domains) in myosin motor proteins
TLDR
This research presents a novel probabilistic procedure that allows for direct measurement of the response of the immune system to earthquake-triggered landsliding.
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Critical assessment of coiled-coil predictions based on protein structure data
TLDR
The most commonly used coiled-coil prediction tools are re-evaluated with respect to the most comprehensive reference data set available, the entire Protein Data Bank, down to each amino acid and its secondary structure to indicate that these predictions should be treated very cautiously and need to be supported and validated by experimental evidence.
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Protein function prediction in genomes: Critical assessment of coiled-coil predictions based on protein structure data
TLDR
The most commonly used coiled-coil prediction tools are re-evaluated with respect to the most comprehensive reference data set available, the entire Protein Data Base (PDB), down to each amino acid and its secondary structure.
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Sequence analysis Waggawagga : comparative visualization of coiled-coil predictions and detection of stable single a-helices ( SAH domains )
TLDR
Waggawagga is a web-based tool for the comparative visualization of coiled-coil predictions and the detection of stable single a-helices (SAH domains) and provides sliders, which can be used to select segments for detailed helical wheel and helical net views.
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