GeneWise and Genomewise
TL;DR: Two algorithms are presented, which predicts gene structure using similar protein sequences, and Genomewise, which provides a gene structure final parse across cDNA- and EST-defined spliced structure.
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Abstract: We present two algorithms in this paper: GeneWise, which predicts gene structure using similar protein sequences, and Genomewise, which provides a gene structure final parse across cDNA- and EST-defined spliced structure. Both algorithms are heavily used by the Ensembl annotation system. The GeneWise algorithm was developed from a principled combination of hidden Markov models (HMMs). Both algorithms are highly accurate and can provide both accurate and complete gene structures when used with the correct evidence.
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Whole genome sequencing of a snailfish from the Yap Trench (~7,000 m) clarifies the molecular mechanisms underlying adaptation to the deep sea.
Yinnan Mu,Chao Bian,Ruoyu Liu,Yuguang Wang,Guangming Shao,Jia Li,Ying Qiu,He Tianliang,Wanru Li,Jingqun Ao,Qiong Shi,Xinhua Chen +11 more
TL;DR: The Yap hadal snailfish (YHS) was captured at a depth of ~7,000 m in the Yap Trench and the final YHS genome assembly was 731.75 Mb.
Complete Genome Sequence of Virulence-Enhancing Siphophage VHS1 from Vibrio harveyi
Krit Khemayan,Anuphap Prachumwat,Anuphap Prachumwat,Burachai Sonthayanon,Burachai Sonthayanon,Aungkul Intaraprasong,Siriporn Sriurairatana,Timothy W. Flegel,Timothy W. Flegel +8 more
TL;DR: The complete, circular genome of VHS1 is presented and annotate, and the last protein was identified as a component of the species-specific toxin mixture described above as being associated with agglutination of hemocytes from P. monodon.
35
Comparative Genomics and Adaptive Selection of the ATP-Binding-Cassette Gene Family in Caenorhabditis Species
TL;DR: A comparative analysis of the ABC family among the three nematode species C. elegans, C. briggsae, and C. remanei found the majority of ABC genes in the three species were found in orthologous trios, indicating that the gene duplication took place before speciation.
35
Chromosome genome assembly and annotation of the yellowbelly pufferfish with PacBio and Hi-C sequencing data.
Yitao Zhou,Shijun Xiao,Gang Lin,Gang Lin,Duo Chen,Cen Wan,Ting Xue,Zhiyu Liu,Jianxing Zhong,Yanting Chen,Yijun Xiao,Jianhua Chen,Yunhai Guo,Youqiang Chen,Yanding Zhang,Xuefeng Hu,Zhen Huang +16 more
TL;DR: The genome resource in this work will be used for the conservation and population genetics of the yellowbelly pufferfish, as well as in vertebrate chromosome evolution studies.
Ancestry and evolution of a secretory pathway serpin.
Abhishek Kumar,Hermann Ragg +1 more
TL;DR: Serpins with the capacity to defend the main cellular export/import routes against uncontrolled endogenous and/or foreign proteolytic activity represent an ancient trait in eukaryotes that has been maintained continuously in metazoans though subtle changes affecting function and subcellular location have evolved.
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Profile hidden Markov models.
TL;DR: Profile HMM methods performed comparably to threading methods in the CASP2 structure prediction exercise and complement standard pairwise comparison methods for large-scale sequence analysis.
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Prediction of Complete Gene Structures in Human Genomic DNA
TL;DR: A general probabilistic model of the gene structure of human genomic sequences which incorporates descriptions of the basic transcriptional, translational and splicing signals, as well as length distributions and compositional features of exons, introns and intergenic regions is introduced.
4.3K
The genome sequence of the filamentous fungus Neurospora crassa
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TL;DR: A high-quality draft sequence of the N. crassa genome is reported, suggesting that RIP has had a profound impact on genome evolution, greatly slowing the creation of new genes through genomic duplication and resulting in a genome with an unusually low proportion of closely related genes.