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GlimmerHMM — ab initio eukaryotic gene finder using a generalized hidden Markov model (GHMM). Predicts gene structures (exons, introns, UTRs, splice sites) in eukaryotic genome sequences from FASTA in
Use with AI
Install the MCP server or CLI to instantly fetch GlimmerHMM documentation:
Install command
claude mcp add biocontext7 -- npx @biocontext7/mcpOr share this page: biocontext7.com/tools/glimmerhmm
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2 shared topics • 1 shared operation
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
2 shared topics • 1 shared operation
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
2 shared topics • 1 shared operation
IsoformSwitchAnalyzeR — R/Bioconductor package for detecting, annotating, and visualizing isoform switches with functional consequences from RNA-seq data. Integrates with Salmon, kallisto, StringTie,
2 shared topics • 1 shared operation
STAR-Fusion — detects candidate fusion transcripts from RNA-seq data using STAR alignments and the FusionInspector validation framework. Integrates with CTAT genome resource libraries for comprehensiv
2 shared topics • 1 shared operation