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SourceForge net transdecoder software version 3.0.1
Transdecoder Software Version 3.0.1, supplied by SourceForge net, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/transdecoder+application/transdecoder+v5+5+0/pmc08704451-190-1-6
Average 90 stars, based on 1 article reviews
transdecoder software version 3.0.1 - by Bioz Stars, 2026-11
90/100 stars

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Software:

Article Title: Shared Patterns of Gene Expression and Protein Evolution Associated with Adaptation to Desert Environments in Rodents
Article Snippet: To identify coding regions within our assembled transcripts for downstream analyses, we utilized TransDecoder v5.5.0 ( http://transdecoder.sourceforge.net ).

Article Title: Comparative Transcriptomics Analysis of the Symbiotic Germination of D. officinale (Orchidaceae) With Emphasis on Plant Cell Wall Modification and Cell Wall-Degrading Enzymes
Article Snippet: TransDecoder (version 5.5; http://transdecoder.sourceforge.net/ ) was used to identify putative coding regions from the assembled unigenes, and only the best-predicted protein was retained for each transcript (single_best_only option).

Article Title: Phylogenomics Resolves the Phylogeny of Theaceae by Using Low-Copy and Multi-Copy Nuclear Gene Makers and Uncovers a Fast Radiation Event Contributing to Tea Plants Diversity.
Article Snippet: TransDecoder v5.5.0 (http://transdecoder.sourceforge. net/ (accessed on 8 November 2021)) was used to predict CDS regions.

Article Title: Chromosome-level genome assemblies of two littorinid marine snails indicate genetic basis of intertidal adaptation and ancient karyotype evolved from bilaterian ancestors
Article Snippet: PASAPIPELINE v2.4.1 [72], STRINGTIE v2.2.1 [73], and TRANSDECODER v5.5.0 (http://transdecoder.sourceforge.net) were used to predict candidate protein-coding regions in two littorinid genomes.

Article Title: The Origin and Evolution of Orphan Genes: A Case Study in Tea Plant Family
Article Snippet: The software TransDecoder version 5.5.0 ( http://transdecoder.sourceforge.net/ , accessed in August 2023) was utilized for the prediction of coding sequence (CDS) regions.

Article Title: Pseudocercospora fijiensis Conidial Germination Is Dominated by Pathogenicity Factors and Effectors.
Article Snippet: Then, assembled transcripts were translated to coding protein sequences using TransDecoder version 5.7.0 (http://transdecoder. sourceforge.net/) with proteins of at least 30 amino acids (peptides) selected for further analysis (Haas, BJ. https://github.com/TransDecoder/TransDecoder’).

Article Title: Recombinant Production and Characterization of a New Toxin from Cryptops iheringi Centipede Venom Revealed by Proteome and Transcriptome Analysis
Article Snippet: The TransDecoder software version 3.0.1 ( http://transdecoder.sourceforge.net/ ; accessed on 15 January 2018) was used to identify Open Reading Frames (ORFs) from the assembled transcripts with protein lengths higher than 60 amino acids.

Article Title: Genomic analysis reveals phylogeny of Zygophyllales and mechanism for water retention of a succulent xerophyte.
Article Snippet: Revealing the genetic basis for stress-resistant traits in extremophile plants will yield important information for crop improvement.. Zygophyllum xanthoxylum, an extant species of the ancient Mediterranean, is a succulent xerophyte that can maintain a favorable water status under desert habitats; however, the genetic basis of this adaptive trait is poorly understood.. Furthermore, the phylogenetic position of Zygophyllales, to which Z. xanthoxylum belongs, remains controversial.

Sequencing:

Article Title: Shared Patterns of Gene Expression and Protein Evolution Associated with Adaptation to Desert Environments in Rodents
Article Snippet: To identify coding regions within our assembled transcripts for downstream analyses, we utilized TransDecoder v5.5.0 ( http://transdecoder.sourceforge.net ).

Article Title: Comparative Transcriptomics Analysis of the Symbiotic Germination of D. officinale (Orchidaceae) With Emphasis on Plant Cell Wall Modification and Cell Wall-Degrading Enzymes
Article Snippet: TransDecoder (version 5.5; http://transdecoder.sourceforge.net/ ) was used to identify putative coding regions from the assembled unigenes, and only the best-predicted protein was retained for each transcript (single_best_only option).

Article Title: Phylogenomics Resolves the Phylogeny of Theaceae by Using Low-Copy and Multi-Copy Nuclear Gene Makers and Uncovers a Fast Radiation Event Contributing to Tea Plants Diversity.
Article Snippet: TransDecoder v5.5.0 (http://transdecoder.sourceforge. net/ (accessed on 8 November 2021)) was used to predict CDS regions.

Article Title: Chromosome-level genome assemblies of two littorinid marine snails indicate genetic basis of intertidal adaptation and ancient karyotype evolved from bilaterian ancestors
Article Snippet: PASAPIPELINE v2.4.1 [72], STRINGTIE v2.2.1 [73], and TRANSDECODER v5.5.0 (http://transdecoder.sourceforge.net) were used to predict candidate protein-coding regions in two littorinid genomes.

Article Title: The Origin and Evolution of Orphan Genes: A Case Study in Tea Plant Family
Article Snippet: The software TransDecoder version 5.5.0 ( http://transdecoder.sourceforge.net/ , accessed in August 2023) was utilized for the prediction of coding sequence (CDS) regions.

Article Title: Pseudocercospora fijiensis Conidial Germination Is Dominated by Pathogenicity Factors and Effectors.
Article Snippet: Then, assembled transcripts were translated to coding protein sequences using TransDecoder version 5.7.0 (http://transdecoder. sourceforge.net/) with proteins of at least 30 amino acids (peptides) selected for further analysis (Haas, BJ. https://github.com/TransDecoder/TransDecoder’).

Article Title: Recombinant Production and Characterization of a New Toxin from Cryptops iheringi Centipede Venom Revealed by Proteome and Transcriptome Analysis
Article Snippet: The TransDecoder software version 3.0.1 ( http://transdecoder.sourceforge.net/ ; accessed on 15 January 2018) was used to identify Open Reading Frames (ORFs) from the assembled transcripts with protein lengths higher than 60 amino acids.

Article Title: Genomic analysis reveals phylogeny of Zygophyllales and mechanism for water retention of a succulent xerophyte.
Article Snippet: Revealing the genetic basis for stress-resistant traits in extremophile plants will yield important information for crop improvement.. Zygophyllum xanthoxylum, an extant species of the ancient Mediterranean, is a succulent xerophyte that can maintain a favorable water status under desert habitats; however, the genetic basis of this adaptive trait is poorly understood.. Furthermore, the phylogenetic position of Zygophyllales, to which Z. xanthoxylum belongs, remains controversial.



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Transdecoder Application, supplied by Unigene, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/transdecoder+application/transdecoder+application/10__1016_slash_j__emcon__2024__100415-126-1-17
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