Retrieve the best hits across species from a BLAST table

This function aims to retrieve the best blast hits for each query sequence by filtering a blast_tbl using the following criteria. A best hit is defined as (fulfilling all three critaria):

• maximum alig_length: only the hit having the longest alignment length is retained.

• qcovhsp >= min_qcovhsp: only hits that have a query coverage of at least min_qcovhsp are retained.

• maximum bit_score: only the hit having the highest bit-score is retained.

filter_best_hits(blast_tbl, min_qcovhsp = 50)

Arguments

blast_tbl

a BLAST table generated with detect_homologs_proteome_to_proteome or detect_homologs_cds_to_cds.

min_qcovhsp

minimum query coverage of the hit in percent 10 to 100 that shall be retained. Default value is set to min_qcovhsp = 50 (= a best hit alignment must have at least 50 percent query coverage).

See also

filter_homologs_core_set, gg_blast_hits, blast_nucleotide_to_nucleotide, blast_protein_to_protein

Author

Hajk-Georg Drost