transdecoder github.io

TransDecoder Find Coding Regions Within Transcripts

TransDecoder Find Coding Regions Within Transcripts. TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks. TransDecoder identifies likely coding sequences based on the following criteria. A minimum length open reading frame ORF is found in a transcript sequence. The software is primarily maintained by Brian Haas.
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LINKS TO TRANSDECODER.GITHUB.IO

EVidenceModeler EVM

EVM provides a flexible and intuitive framework for combining diverse evidence types into a single automated gene structure annotation system. To fully leverage high quality transcript alignments, you should download and install PASA.

Trinotate Transcriptome Functional Annotation and Analysis

Is becoming more useful, the interface was given a facelift including other various performance improvements.

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TransDecoder Find Coding Regions Within Transcripts

DESCRIPTION

TransDecoder Find Coding Regions Within Transcripts. TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks. TransDecoder identifies likely coding sequences based on the following criteria. A minimum length open reading frame ORF is found in a transcript sequence. The software is primarily maintained by Brian Haas.

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The site had the following in the web page, "TransDecoder Find Coding Regions Within Transcripts." I observed that the web site stated " TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks." They also stated " TransDecoder identifies likely coding sequences based on the following criteria. A minimum length open reading frame ORF is found in a transcript sequence. The software is primarily maintained by Brian Haas."

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