De novo transcriptome assembly of shrimp Palaemon serratus
Sign Up to like & getrecommendations! Published in 2017 at "Genomics Data"
DOI: 10.1016/j.gdata.2016.12.009
Abstract: The shrimp Palaemon serratus is a coastal decapod crustacean with a high commercial value. It is harvested for human consumption. In this study, we used Illumina sequencing technology (HiSeq 2000) to sequence, assemble and annotate… read more here.
Keywords: palaemon serratus; novo transcriptome; serratus; transcriptome assembly ... See more keywords
De novo transcriptome assembly for the lung of the ornamented pygmy frog (Microhyla fissipes)
Sign Up to like & getrecommendations! Published in 2017 at "Genomics Data"
DOI: 10.1016/j.gdata.2017.07.002
Abstract: Microhyla fissipes, belonging to Neobatrachia, is a new model organism to study developmental biology, adaptive mechanisms from aquatic to terrestrial life, environmental toxicology, and human disease. M. fissipes use of lungs soon after hatching makes… read more here.
Keywords: novo transcriptome; transcriptome assembly; assembly lung; microhyla fissipes ... See more keywords
De novo transcriptome assembly of a facultative parasitic nematode Pelodera (syn. Rhabditis) strongyloides.
Sign Up to like & getrecommendations! Published in 2019 at "Gene"
DOI: 10.1016/j.gene.2019.05.041
Abstract: Pelodera strongyloides is a generally free-living gonochoristic facultative nematode. The whole genomic sequence of P. strongyloides remains unknown but 4 small subunit ribosomal RNA (ssrRNA) gene sequences are available. This project launched a de novo… read more here.
Keywords: novo transcriptome; pelodera; transcriptome assembly; rna ... See more keywords
De novo transcriptome assembly and comparative analysis between male and benzyladenine-induced female inflorescence buds of Plukenetia volubilis.
Sign Up to like & getrecommendations! Published in 2018 at "Journal of plant physiology"
DOI: 10.1016/j.jplph.2017.12.006
Abstract: Plukenetia volubilis is a promising oilseed crop due to its seeds being rich in unsaturated fatty acids, especially alpha-linolenic acid. P. volubilis is monoecious, with separate male and female flowers on the same inflorescence. We… read more here.
Keywords: novo transcriptome; plukenetia volubilis; transcriptome assembly; inflorescence ... See more keywords
De novo transcriptome assembly and preliminary analyses of two avian malaria parasites, Plasmodium delichoni and Plasmodium homocircumflexum.
Sign Up to like & getrecommendations! Published in 2018 at "Genomics"
DOI: 10.1016/j.ygeno.2018.12.004
Abstract: Parasites of the genus Plasmodium infect a wide array of hosts, causing malaria in all major groups of terrestrial vertebrates including primates, reptiles, and birds. Molecular mechanisms explaining why some Plasmodium species are virulent, while… read more here.
Keywords: delichoni; transcriptome assembly; two avian; homocircumflexum ... See more keywords
De novo transcriptome assembly and protein profiling of copper-induced lignocellulolytic fungus Ganoderma lucidum MDU-7 reveals genes involved in lignocellulose degradation and terpenoid biosynthetic pathways.
Sign Up to like & getrecommendations! Published in 2019 at "Genomics"
DOI: 10.1016/j.ygeno.2019.01.012
Abstract: Ganoderma lucidum is an important medicinal fungus that possesses exceedingly high lignocellulose degrading ability. Evidently, Cu2+ has decisive roles on the mycelial growth and enzyme production. To reveal the effect of Cu2+ on G. lucidum… read more here.
Keywords: novo transcriptome; fungus; ganoderma lucidum; transcriptome assembly ... See more keywords
De novo transcriptome assembly and identification of G-Protein-Coupled-Receptors (GPCRs) in two species of monogenean parasites of fish
Sign Up to like & getrecommendations! Published in 2022 at "Parasite"
DOI: 10.1051/parasite/2022052
Abstract: Genomic resources for Platyhelminthes of the class Monogenea are scarce, despite the diversity of these parasites, some species of which are highly pathogenic to their fish hosts. This work aimed to generate de novo-assembled transcriptomes… read more here.
Keywords: novo transcriptome; receptors gpcrs; transcriptome assembly; coupled receptors ... See more keywords
TransRef enables accurate transcriptome assembly by redefining accurate neo-splicing graphs.
Sign Up to like & getrecommendations! Published in 2021 at "Briefings in bioinformatics"
DOI: 10.1093/bib/bbab261
Abstract: RNA-seq technology is widely employed in various research areas related to transcriptome analyses, and the identification of all the expressed transcripts from short sequencing reads presents a considerable computational challenge. In this study, we introduce… read more here.
Keywords: assembly redefining; accurate transcriptome; neo splicing; transcriptome assembly ... See more keywords
De novo transcriptome assembly: A comprehensive cross-species comparison of short-read RNA-Seq assemblers
Sign Up to like & getrecommendations! Published in 2019 at "GigaScience"
DOI: 10.1093/gigascience/giz039
Abstract: Abstract Background In recent years, massively parallel complementary DNA sequencing (RNA sequencing [RNA-Seq]) has emerged as a fast, cost-effective, and robust technology to study entire transcriptomes in various manners. In particular, for non-model organisms and… read more here.
Keywords: novo transcriptome; rna seq; transcriptome assembly;
MultiTrans: An Algorithm for Path Extraction Through Mixed Integer Linear Programming for Transcriptome Assembly
Sign Up to like & getrecommendations! Published in 2022 at "IEEE/ACM Transactions on Computational Biology and Bioinformatics"
DOI: 10.1109/tcbb.2021.3083277
Abstract: Recent advances in RNA-seq technology have made identification of expressed genes affordable, and thus boosting repaid development of transcriptomic studies. Transcriptome assembly, reconstructing all expressed transcripts from RNA-seq reads, is an essential step to understand… read more here.
Keywords: path extraction; transcriptome assembly; mixed integer;
TransPi - a comprehensive TRanscriptome ANalysiS PIpeline for de novo transcriptome assembly.
Sign Up to like & getrecommendations! Published in 2022 at "Molecular ecology resources"
DOI: 10.1111/1755-0998.13593
Abstract: The use of RNA-Seq data and the generation of de novo transcriptome assemblies have been pivotal for studies in ecology and evolution. This is distinctly true for non-model organisms, where no genome information is available.… read more here.
Keywords: analysis; transcriptome assembly; transcriptome; novo transcriptome ... See more keywords