a program to find cross-reactive epitopes 8000 with structural information from known protein structures.
CRESSP requires BLASTP from BLAST+ and HMMER3, which can be installed through conda with the following commands:
conda install -c bioconda blast
conda install -c bioconda hmmerCRESSP can be installed from PyPI (https://pypi.org/project/cressp/)
pip install cresspusage: cressp [-h] [-t DIR_FILE_PROTEIN_TARGET] [-q DIR_FILE_PROTEIN_QUERY] [-o DIR_FOLDER_OUTPUT] [-c CPU] [-w WINDOW_SIZE] [-s FLOAT_THRES_AVG_SCORE_BLOSUM_WEIGHTED] [-e FLOAT_THRES_E_VALUE] [-H]
[-d DIR_FILE_QUERY_HMMDB] [-Q]
arguments:
-h, --help show this help message and exit
-t DIR_FILE_PROTEIN_TARGET, --dir_file_protein_target DIR_FILE_PROTEIN_TARGET
(Required) an input FASTA file containing target protein sequences.
-q DIR_FILE_PROTEIN_QUERY, --dir_file_protein_query DIR_FILE_PROTEIN_QUERY
(Default: UniProt human proteins) an input FASTA file containing query protein sequences.
-o DIR_FOLDER_OUTPUT, --dir_folder_output DIR_FOLDER_OUTPUT
(Default: a subdirectory of the current directory) an output directory
-c CPU, --cpu CPU (Default: 1) Number of logical CPUs (threads) to use in the current compute node.
-w WINDOW_SIZE, --window_size WINDOW_SIZE
(Default: 30) list of window sizes separated by comma. Example: 15,30,45
-s FLOAT_THRES_AVG_SCORE_BLOSUM_WEIGHTED, --float_thres_avg_score_blosum_weighted FLOAT_THRES_AVG_SCORE_BLOSUM_WEIGHTED
(Default: 0.15) threshold for average weighted BLOSOM62 alignment score for filtering aligned sequences
-e FLOAT_THRES_E_VALUE, --float_thres_e_value FLOAT_THRES_E_VALUE
(Default: 1e-20) threshold for the global alignment e-value in a scientific notation Example: 1e-3
-H, --flag_use_HMM_search
(Default: False) Set this flag to perform HMM search in addition to BLASTP search. HMM profile search is performed with HMMER3. The search usually takes several hours for
metagenome-assembled genomes
-d DIR_FILE_QUERY_HMMDB, --dir_file_query_hmmdb DIR_FILE_QUERY_HMMDB
(Default: a HMM profile database of 1012 human proteins searched against UniProt Pan Proteomes. These proteins consist of experimentally validated human autoantigens) a file
containing HMM DB of query proteins aligned against pan-proteomes
-Q, --flag_skip_struc_prop_for_protein_target
(Default: False) Set this flag to skip the estimation of structural properties of target proteins. Only structural properties of query proteins will be used to calculate
accessibility-weighted-similarity scoresDownload the proteome of SARS-CoV-2 from UniProt (UP000464024) as a fasta sequence
run the following command to
- Search SARS-CoV-2 protein sequences with human protein sequences with BLASTP and HMMER3, and
- Calculate similarity scores based on relative-surface-availability of residues of human proteins
cressp -t UP000464024_2697049.fasta.gz --flag_use_HMM_search --FLOAT_THRES_E_VALUE 5e-2 --cpu 2