GPCR-PEn Instructions

Select your sequence type:

Our prediction ensemble has two different variations dependent on sequence type. See the descriptions below to determine which option best suits your data:

Submit your sequence(s):

You will need your sequence(s) in FASTA format. This can either be in a file or you may paste it into the submission box. If you are unfamiliar with FASTA format please see the example below:
>sequence_name
MSFSSRWDCMCRNERAVSLAIELNEKLQRILNRHKDLLSGKITVPGRSTTSNGHKKLELNASTANSSISN
Currently, there is no limit to sequence length or number of sequences in a file, but larger files will take longer to process.

Choose your prediction tools:

By default, GPCR-PEn will use the available tool Log-Reg. If you would like to use a combination of tools only select which ones you prefer.

Tool Specific Parameter Selection:

The default parameters used by GPCR-PEn are the ones used in [insert citation to Synganglion paper here]. However, you may wish to alter the following parameters:
ORF-Finder Parameters:
BLAST/PFAM GPCRTm Parameters: GPCR-PEn differentiates between full/possibly full sequences and partial/fragment sequences using length and number of predicted helices. The minimum number of helices for a full length sequence is 6. This is due to the fact that TMHMM occasionally misses a helix even if 7 are present. Additionally, TMHMM will occasionally detect an additional helix as well. If you are curious how the various parameters are used in our prediction ensemble, please view the diagrams below: If you are curious how the various parameters are used in our prediction ensemble, please view the diagrams below:

DNA SEQUENCE(S) WORKFLOW
GPCR Pipeline for DNA

PROTEIN SEQUENCE(S) WORKFLOW
GPCR Pipeline for Proteins


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This work is supported in part by the NIMHD grant 5G12MD007592 to the UTEP Border Biomedical Center.
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