nf-core/isoseq: simple gene and isoform annotation with PacBio Iso-Seq long-read sequencing
Sign Up to like & getrecommendations! Published in 2023 at "Bioinformatics"
DOI: 10.1093/bioinformatics/btad150
Abstract: Abstract Motivation Iso-Seq RNA long-read sequencing enables the identification of full-length transcripts and isoforms, removing the need for complex analysis such as transcriptome assembly. However, the raw sequencing data need to be processed in a… read more here.
Keywords: core; core isoseq; read sequencing; long read ... See more keywords
PRAPI: post-transcriptional regulation analysis pipeline for Iso-Seq
Sign Up to like & getrecommendations! Published in 2018 at "Bioinformatics"
DOI: 10.1093/bioinformatics/btx830
Abstract: Summary The single-molecule real-time (SMRT) isoform sequencing (Iso-Seq) based on Pacific Bioscience (PacBio) platform has received increasing attention for its ability to explore full-length isoforms. Thus, comprehensive tools for Iso-Seq bioinformatics analysis are extremely useful.… read more here.
Keywords: iso; analysis; iso seq; prapi post ... See more keywords
Unveiling the transcriptomic complexity of Miscanthus sinensis using a combination of PacBio long read- and Illumina short read sequencing platforms
Sign Up to like & getrecommendations! Published in 2021 at "BMC Genomics"
DOI: 10.1186/s12864-021-07971-x
Abstract: Background Miscanthus sinensis Andersson is a perennial grass that exhibits remarkable lignocellulose characteristics suitable for sustainable bioenergy production. However, knowledge of the genetic resources of this species is relatively limited, which considerably hampers further work… read more here.
Keywords: sinensis; pacbio iso; pacbio; iso seq ... See more keywords
Reconstruction of the full-length transcriptome atlas using PacBio Iso-Seq provides insight into the alternative splicing in Gossypium australe
Sign Up to like & getrecommendations! Published in 2019 at "BMC Plant Biology"
DOI: 10.1186/s12870-019-1968-7
Abstract: BackgroundGossypium australe F. Mueller (2n = 2x = 26, G2 genome) possesses valuable characteristics. For example, the delayed gland morphogenesis trait causes cottonseed protein and oil to be edible while retaining resistance to biotic stress. However, the lack of… read more here.
Keywords: iso seq; alternative splicing; full length; length transcriptome ... See more keywords
Extensive Variation in Gene Expression is Revealed in 13 Fertility-Related Genes Using RNA-Seq, ISO-Seq, and CAGE-Seq From Brahman Cattle
Sign Up to like & getrecommendations! Published in 2022 at "Frontiers in Genetics"
DOI: 10.3389/fgene.2022.784663
Abstract: Fertility is a key driver of economic profitability in cattle production. A number of studies have identified genes associated with fertility using genome wide association studies and differential gene expression analysis; however, the genes themselves… read more here.
Keywords: expression; fertility; variation; iso seq ... See more keywords
Integrative analysis of Iso-Seq and RNA-seq reveals dynamic changes of alternative promoter, alternative splicing and alternative polyadenylation during Angiotensin II-induced senescence in rat primary aortic endothelial cells
Sign Up to like & getrecommendations! Published in 2023 at "Frontiers in Genetics"
DOI: 10.3389/fgene.2023.1064624
Abstract: In eukaryotes, alternative promoter (AP), alternative splicing (AS), and alternative polyadenylation (APA) are three crucial regulatory mechanisms that modulate message RNA (mRNA) diversity. Although AP, AS and APA are involved in diverse biological processess, whether… read more here.
Keywords: seq; dynamic changes; rna; senescence ... See more keywords
Integrative analysis of Iso-Seq and RNA-seq data reveals transcriptome complexity and differentially expressed transcripts in sheep tail fat
Sign Up to like & getrecommendations! Published in 2021 at "PeerJ"
DOI: 10.7717/peerj.12454
Abstract: Background Nowadays, both customers and producers prefer thin-tailed fat sheep. To effectively breed for this phenotype, it is important to identify candidate genes and uncover the genetic mechanism related to tail fat deposition in sheep.… read more here.
Keywords: tail fat; seq data; iso seq; fat ... See more keywords