Reference

Methods to run searchers in the HMMER web
search_hmmscan()	Perform a hmmscan search of a protein sequence against a profile-HMM database.
search_hmmsearch()	Perform a hmmsearch search of a protein sequence against a protein sequence database.
search_phmmer()	Perform a phmmer search of a protein sequence against a protein sequence database.
Parsering methods
parse_fasta_headers()	Extracts the sequence identifier from the recognized fasta sequence headers.
read_hmmer_from_json()	Read the results of a search with HMMER from an json file.
extract_from_hmmer()	Split a column composed of nested lists into multiple columns.
Filtering output methods
filter_hmmer()	Filter dataframe depending on a column and a threshold.
Methods to add information into the HMMER output
add_physicochemical_properties_to_HMMER_tbl()	Add EMBOSS-inspired theoretical physicochemical properties using the Peptides library to an AnnotatedDataFrame
add_sequences_to_hmmer_tbl()	Add sequences from one of the output files from HMMER server to a Data Frame obtained by searching in HMMER.
add_taxa_to_hmmer_tbl()	Add taxonomic information to a Data Frame obtained from HMMER with a "hits.taxid" column.
annotate_with_NCBI_taxid()	Retrieve the taxonomic data for a given NCBI taxon ID using a local database or as remote data sources.
pairwise_alignment_sequence_identity()	Calculate the percentage of pairwise sequence identity
Graphical Utilities
hmmer_evalues_cleveland_dot_plot()	A Cleveland dot plot with the evalues of the domains and sequences.
pairwise_sequence_identity_heatmap()	Plot a heatmap with the pairwise identity percentages.
pairwise_sequence_identity_histogram()	Plot a histogram with the pairwise identity percentages (without the diagonal).
Dataframe examples
hmmscan_2abl	hmmscan_2abl
phmmer_2abl	phmmer_2abl