LipoSearch-GFF v2

StepAnnotation
Step 1: Input dataset
select at runtime
Step 2: Get open reading frames (ORFs) or coding sequences (CDSs)
Output dataset 'output' from step 1
11. Bacterial
Look for CDSs (with start and stop codons)
30
Search both the forward and reverse strand
Step 3: GFF3 Feature Sequence Export
From History
Output dataset 'output' from step 1
Output dataset 'out_gff3_file' from step 2
CDS
True
Step 4: GFF3 Add Gene to CDS
Output dataset 'out_gff3_file' from step 2
Step 5: Fasta Translate
Output dataset 'default' from step 3
Protein
[11] The Bacterial, Archaeal and Plant Plastid Code
True
False
Step 6: GFF3 Filter: Require Phage Start
From History
Output dataset 'output' from step 1
Output dataset 'output' from step 4
Step 7: TMHMM (GFF3)
Output dataset 'default' from step 5
Step 8: Identify Lipoboxes
Output dataset 'stdout' from step 6
Output dataset 'output' from step 1
10
60
Step 9: Rebase GFF3 features
Output dataset 'out_gff3_file' from step 2
Output dataset 'output' from step 7
False
True
ID
Step 10: Intersect
Output dataset 'default' from step 9
Output dataset 'default' from step 8
Step 11: Remove Annotation Feature
Output dataset 'oa' from step 10
True
True

No value found for 'Remove 'region' features'. Using default: 'True'.
Step 12: Remove Annotation Feature
Output dataset 'ob' from step 10
True
True

No value found for 'Remove 'region' features'. Using default: 'True'.