A Deep Learning Model for Transmembrane Topology Prediction and Classification
Input
name:type
description
pattern
meta
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
fasta
:file
Database of sequences in FASTA format
*.{fasta,fa,fasta.gz,fa.gz}
Output
name:type
description
pattern
gff3
meta
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
biolib_results/TMRs.gff3
:file
Predicted topologies (inside, outside, TMhelix) in general Feature Format Version 3
biolib_results/TMRs.gff3
line3
meta
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
biolib_results/predicted_topologies.3line
:file
Predicted topologies and information of protein sequences in three lines (name, sequence, topology)
biolib_results/predicted_topologies.3line
md
meta
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
biolib_results/deeptmhmm_results.md
:file
Markdown results file
biolib_results/deeptmhmm_results.md
csv
meta
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
biolib_results/*_probs.csv
:file
CSV file with per-residue predictions for the likelihood of each amino acid being in structural regions such as Beta-sheet, Periplasm, Membrane, Inside, Outside or Signal (only when querying against genomic fasta)
biolib_results/*_probs.csv
png
meta
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
biolib_results/plot.png
:file
Most likely topology probability line plots (only when querying against genomic fasta)
biolib_results/plot.png
versions_biolib
${task.process}
:string
The name of the process
biolib
:string
The name of the tool
biolib --version 2>&1 | sed 's/.*version //'
:eval
The expression to obtain the version of the tool
versions_python
${task.process}
:string
The name of the process
python
:string
The name of the tool
python --version | sed 's/Python //'
:eval
The expression to obtain the version of the tool
Topics
name:type
description
pattern
versions
${task.process}
:string
The name of the process
biolib
:string
The name of the tool
biolib --version 2>&1 | sed 's/.*version //'
:eval
The expression to obtain the version of the tool
${task.process}
:string
The name of the process
python
:string
The name of the tool
python --version | sed 's/Python //'
:eval
The expression to obtain the version of the tool
Tools
deeptmhmm
MIT
Deep Learning model for Transmembrane Helices protein domain prediction through the BioLib Python Client
