Contact Prediction¶

The script to run contact prediction using HHblits to generate your sequence alignment and CCMpred to predict the contacts is called conkit-predict. You can run this script using two different modes.

1. Starting with a sequence

$> conkit-predict seq <path/to/ccmpred> <path/to/hhblits> <path/to/hhblits_database> toxd/toxd.fasta fasta

The call above uses your sequence file toxd/toxd.fasta in fasta format to first generate a Multiple Sequence Alignment. It will then analyse your alignment identical to the conkit-msatool script. It will also sort out all the required conversions before executing CCMpred to run the contact prediction. Finally, it will analyse your contact prediciton and plot a contact map, just like the conkit-plot script does.

2. Starting with a Multiple Sequence Alignment

$> conkit-predict aln <path/to/ccmpred> toxd/toxd.a3m a3m

This call performs identical operations to the full call under point 1, except that it skips the generation of the alignment. This might be particularly useful if you have limited disk space and cannot store the rather large sequence database that HHblits requires. You can generate your alignment using online servers, such as the HHblits Server or the Jackhmmer Server. Both formats are accepted by ConKit, the keywords can be found in the Table of available file formats.