TransDecoder — identifies candidate coding regions within transcript sequences from de novo RNA-Seq assemblies. Provides TransDecoder.LongOrfs for extracting long open reading frames and TransDecoder.
Use with AI
Install the MCP server or CLI to instantly fetch TransDecoder documentation:
Install command
claude mcp add biocontext7 -- npx @biocontext7/mcpOr share this page: biocontext7.com/tools/transdecoder
gffread -- GFF/GTF utility for filtering, converting, and extracting sequences from genome annotation files. Converts between GFF3 and GTF formats, extracts transcript (FASTA) and protein sequences fr
3 shared topics • 1 shared operation
MAKER — portable genome annotation pipeline that integrates ab initio gene predictors (SNAP, Augustus, GeneMark), protein and EST evidence alignment, and repeat masking to produce GFF3 gene models wit
3 shared topics • 1 shared operation
>
3 shared topics
BRAKER — fully automated gene structure annotation pipeline combining GeneMark-ES/ET/EP/ETP with AUGUSTUS training. Supports RNA-Seq evidence (BRAKER1), protein evidence (BRAKER2), and combined RNA-Se
3 shared topics
GeMoMa (Gene Model Mapper) is a Java-based homology-driven gene prediction tool for eukaryotic genome annotation. Uses protein and CDS sequences from annotated reference species to predict gene models
3 shared topics