GPCR Pipeline Instructions

Select your sequence type:

Our pipeline has three 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 pipeline will use all the available tools (GPCRTm, BLAST, GPCRpred, PFAM). If you would only like to use a subset of the tools only select which ones you prefer.

Tool Specific Parameter Selection:

The default parameters used by GPCR Pipeline 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 Pipeline 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 pipeline, please view the diagrams below: If you are curious how the various parameters are used in our pipeline, 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 by the USDA-NIFA grant 2012-38422-19910, and the NIMHD grant 2G12MD007592
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