Galaxy |

Merge gff using gffutils (version 1.0)

Peptides coordinates:

Peptides prediction coordinates in gff format

BLASTP: Peptides vs related species:

[optional] NCBI BLAST+ blastp output. Output format: XML

BLASTX: Transcripts vs related species:

[optional] NCBI BLAST+ blastx output. Output format: XML

HMMER hmmscan: Peptides vs PFAM:

[optional] HMMER hmmscan output: Table of per-domain hits. Output format: Table of per-domain hits (--domtblout)

TMHMM on Peptides:

[optional]

SignalP on Peptides:

[optional]

Filter options

Filter options 0

Keep the sqlite database file:

Can be used for visualization purpose

What it does

This tool loads annotations from multiple tools into a gffutils sqlite database and outputs a single gff file containing all annotations. The sqlite db can be used for filtering and visualization.

Based on https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate

Suggested upstream Galaxy tools

Transcripts

Trinity: iuc/trinity

Peptides

TransDecoder: iuc/transdecoder

Genes to transcripts map

Generate gene to transcript map for Trinity assembly: iuc/trinity_gene_to_trans_map

BLASTP: Peptides vs Uniprot.SwissProt

NCBI BLAST+ blastp: devteam/ncbi_blast_plus

BLASTX: Transcripts vs Uniprot.SwissProt

NCBI BLAST+ blastx: devteam/ncbi_blast_plus

HMMER hmmscan: Peptides vs PFAM

HMMER hmmscan: iuc/hmmer_hmmscan

TMHMM on Peptides

TMHMM 2.0: peterjc/tmhmm_and_signalp

SignalP on Peptides

SignalP 3.0: peterjc/tmhmm_and_signalp