Transcriptome assembly and annotation
De novo transcriptome assembly, functional annotation and differential gene expression analysis of juvenile and adult E. fetida, a model oligochaete used in ecotoxicological studies
... novo transcriptome assembly of ...functional annotation of the Trinity generated transcriptome file and the trans- decoder generated peptide sequence file along with BLASTX, BLASTP and HMMER ...
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A computational framework for transcriptome assembly and annotation in non-model organisms: the case of venturia inaequalis
... 66 3.0 Abstract Downstream analyses of short-reads from next-generation sequencing platforms are often preceded by a pre-processing step that removes uncalled and wrongly called bases. Standard approaches rely on their ...
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Transcriptome Assembly, Gene Annotation and Tissue Gene Expression Atlas of the Rainbow Trout
... by transcriptome information that will enhance genome assembly and ...Previously, transcriptome reference sequences were reported using data from different ...well-annotated transcriptome is ...
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Improved Annotation with de novo Transcriptome Assembly in Four Social Amoeba Species
... 17. Felder M, A. Romualdi, A. Petzold, M. Platzer, J. Sühnel and G. Glöckner GenColors-based 629 comparative genome databases for small eukaryotic genomes. Nucleic acids research 630 2013, 41(Database issue):D692-699. ...
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De novo transcriptome assembly, annotation and comparison of four ecological and evolutionary model salmonid fish species
... initial assembly, strict filtering was used to remove duplicated, redundant, and low confidence ...available. Assembly completeness was assessed using three approaches, all of which supported high quality ...
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De-novo transcriptome assembly for gene identification, analysis, annotation, and molecular marker discovery in Onobrychis viciifolia
... The assembly, allowed us to identify 3786 ...novo assembly was easier to address than the development of SNPs, which is challenging with- out a reference ...combined assembly was used to align the ...
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Bayesian transcriptome assembly
... For simulated data, Bayesembler markedly outper- formed all other assemblers on both sensitivity and preci- sion, with IsoLasso coming in as runner-up. Interestingly, Bayesembler was markedly better at estimating the ...
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Assembly and annotation of a non model gastropod (Nerita melanotragus) transcriptome: a comparison of De novo assemblers
... for transcriptome assembly from Illumina short reads, nonetheless their effectiveness for de novo assembly of Ion Torrent data remains relatively unexplored as the Ion Torrent technology is newer and ...
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Assembly and annotation of a non-model gastropod (Nerita melanotragus) transcriptome: a comparison of De novo assemblers
... for transcriptome assembly from Illumina short reads, nonetheless their effectiveness for de novo assembly of Ion Torrent data remains relatively unexplored as the Ion Torrent technology is newer and ...
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De novo assembly, functional annotation, and analysis of the giant reed (Arundo donax L.) leaf transcriptome provide tools for the development of a biofuel feedstock
... RNA-Seq assembly facilitates the study of transcriptomes for plant species without sequenced genomes, but it is challenging to select the most accurate assembly in this ...
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Transcriptome assembly from long read RNA seq alignments with StringTie2
... guide annotation, we ran StringTie2 and FLAIR on the human chromosome 19 ONT data using random samples of the chromosome 19 annotation, which we varied to contain from 1 to 100% of the ...of ...
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De Novo Transcriptome Assembly For The Tropical Grass Panicum Maximum Jacq.
... because of the smaller number of proteins in this more reliable protein bank. The Phytozome grass protein database comparison displayed a slightly higher number of hits (26,319, 68.91%) than the nr search, mostly ...
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De novo assembly and characterization of the transcriptome in the desiccation tolerant moss Syntrichia caninervis
... caninervis transcriptome using next-generation, RNA-Seq ...novo transcriptome assembly generated 92,240 unigene se- ...GO annotation of the S. caninervis transcriptome and comparison ...
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TransComb: genome guided transcriptome assembly via combing junctions in splicing graphs
... However, these methods achieve sparsity by thresholding transcript expression levels, which results in penalizing low expression transcripts. Bayesembler is a very recently published probabilistic method for both ...
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Assembly, annotation, and polymorphic characterization of the Erysiphe necator transcriptome
... which assembly provided the most potentially relevant sequences, we chose to analyze reciprocal sequence similarity between each assembly and the Bgh protein ...novo assembly was the best Mira ...
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Complete assembly of the Leishmania donovani (HU3 strain) genome and transcriptome annotation
... donovani transcriptome will allow to carry out transcriptome profiling associated with drug resistance in this species without the necessity of using data derived from other Leishmania species 59,91 ...
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De novo assembly, characterization, functional annotation and expression patterns of the black tiger shrimp (Penaeus monodon) transcriptome
... a transcriptome based on eight tissues was assembled for the less well studied banana shrimp Fenneropenaeus merguiensis 24 , and genes involved in early embryonic specification have been studied in Marsupenaeus ...
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Assembly and analysis of the miscanthus ?? giganteus transcriptome
... and assembly of any organism‘s transcriptome establishes a significant base from which many future studies can be ...their assembly establishes a catalog of the genes present in the organism‘s ...
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Functional characterization and annotation of trait-associated genomic regions by transcriptome analysis
... One of the most crucial issues to deal with in genomics is the ambiguity arising from sequence homology. As have been shown in the section of repetitive sequence and sequence complexity, duplicated DNA sequence of ...
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Ten steps to get started in Genome Assembly and Annotation
... assembled transcriptome, or per- haps a re-sequencing approach based on the genomic sequence of a related species, can be enough to answer your scientific ...
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