Human rhinoviruses (HRV), the most frequent cause of respiratory infections, include 99 different serotypes segregating into two species, A and B. Rhinoviruses share extensive genomic sequence similarity with enteroviruses and both are part of the picorn
Full genome sequences are increasingly used to track the geographic spread and transmission dynamics of viral pathogens. Here, with a focus on Israel, we sequence 212 SARS-CoV-2 sequences and use them to perform a comprehensive analysis to trace the origins and spread of the virus. We find ...
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The reliance on a solitary linear reference genome has imposed a significant constraint on our comprehensive understanding of genetic variation in animals. This constraint is particularly pronounced for non-reference sequences (NRSs), which have not been extensively studied. Results In this study, we ...
It is important to highlight that these major transcripts are not always the longest possible for the gene (40% of the major transcripts in primary tissues and 30% in cell lines are not the longest annotated), nor always include the longest CDS (Coding DNA Sequence; approximately 50% of ...
To support gene discovery and gene model verification in the genome of the wheat leaf rust fungus, Puccinia triticina (Pt), we have generated Expressed Sequence Tags (ESTs) by sampling several life cycle stages. We focused on several spore stages and isolated haustorial structures from infected ...
Farh KKH. Predicting splicing from primary sequence with deep learning. Cell. 2019;176(3):535–548. Rentzsch P, Witten D, Cooper GM, et al. CADD: predicting the deleteriousness of variants throughout the human genome. Nucleic Acids Res. 2019;47(D1):D886–94. Article CAS PubMed Google...
Reconstructing full-length transcripts from high-throughput RNA sequencing data is difficult without a reference genome sequence. Grabherr et al. describe Trinity, an algorithm for assembling full-length transcripts from short reads without first mapping
Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol. 2011;29:644–52. Article CAS PubMed PubMed Central Google Scholar Li W, Godzik A. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics...
Sequence alignments between the human reference sequence, GRCh37, and the genomes of Venter and Watson. Variation data are highlighted in green and indicated by an IUPAC code. A. The default display replaces nucleotides with dots if the genome has the same allele as the reference assembly. B....