Perform Massive Local BLAST Searches
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Documentation for package ‘metablastr’ version 0.3.2
Help Pages
| blast2bed | Export BLAST output table to BED file |
| blast_best_hit | Retrieve only the best BLAST hit for each query |
| blast_best_reciprocal_hit | Retrieve only the best reciprocal BLAST hit for each query |
| blast_genomes | Perfrom BLAST Searches Against a Set of Genomes |
| blast_nucleotide_to_genomes | Perfrom BLAST Searches Against a Set of Genomes |
| blast_nucleotide_to_nucleotide | Perform Nucleotide to Nucleotide BLAST Searches (BLASTN) |
| blast_nucleotide_to_protein | Perform Nucleotide to Protein BLAST Searches (BLASTX) |
| blast_protein_to_nr_database | Perform Protein to Protein BLAST Searches Against the NCBI NR Database |
| blast_protein_to_nucleotide | Perform Protein to Nucleotide BLAST Searches (TBLASTN) |
| blast_protein_to_protein | Perform Protein to Protein BLAST Searches (BLASTP) |
| blast_protein_to_proteomes | Perfrom BLAST Searches Against a Set of Proteomes |
| blast_repbase | Query the RepBase to annotate putative LTRs |
| blast_rpsblast | Perform Reverse PSI-BLAST searches (rpsblast) |
| detect_homologs_cds_to_cds | Perform CDS to CDS BLAST Searches against a set of CDS files |
| detect_homologs_proteome_to_proteome | Perform Proteome to Proteome BLAST Searches against a set of Proteomes |
| extract_hit_seqs_from_genomes | Extract sequences of BLAST hits in respective genomes and store it as 'fasta' file(s) |
| extract_promotor_seqs_from_genome | Retrieve all upstream promotor sequences from a genome |
| extract_random_seqs_from_genome | Extract random loci from a genome of interest |
| extract_random_seqs_from_multiple_genomes | Extract random loci from a set of genomes |
| extract_upstream_promotor_seqs | Retrieve all upstream promotor sequences from a genome |
| file_contains_aa | Helper function to check whether input file contains amino acids as required |
| file_contains_dna | Helper function to check whether input file contains dna as required |
| filter_best_hits | Retrieve the best hits across species from a BLAST table |
| filter_homologs_core_set | Retrieve a core set of best hits that is shared across species |
| filter_homologs_core_set_n_species | Retrieve a core set of best hits that is shared across at least N species |
| gg_blast_hits | Plot 'blast_nucleotide_to_genomes' Result |
| gg_blast_hits_summary | Plot 'blast_nucleotide_to_genomes' Result |
| gg_hits_boxplot | Boxplot of a 'blast_tbl' generated with 'detect_homologs_genome_to_genome' or 'detect_homologs_proteome_to_proteome' |
| gg_homologs_one_to_one | Plot number of BLAST hits per species as barplot from a 'tibble' generated with 'detect_homologs_genome_to_genome' or 'detect_homologs_proteome_to_proteome' |
| gg_pairwise_orthologs_line | Plot number of pairwise orthologs for multiple species comparisons |
| gg_species_dnds_blast_tbl | Plot pairwise dN, dS, or dN/dS distributions of orthologous genes |
| gg_species_feature_blast_tbl | Plot pairwise feature distributions of orthologous genes |
| gg_species_promotor_dist_blast_tbl | Plot pairwise promotor sequence distance distributions of orthologous genes |
| list_outformats | List available BLAST output formats |
| motif_compare | Count the number of motifs in a set of non-random versus random sequences |
| motif_compare_multi | Count the number of motifs in a set of non-random versus randomly sampled genomic sequences for multiple species |
| motif_compare_multi_promotor_seqs | Count the number of motifs in a set of non-random versus randomly drawn gene promotor sequences for multiple species |
| motif_count | Count the number of motifs in a set of sequences |
| motif_count_matrix | Count the number of motifs in a set of sequences and generate a motif count matrix |
| motif_enrichment | Test motif enrichment in a set of non-random versus random sequences |
| motif_enrichment_multi | Statistical assessment of motif enrichments in a set of non-random versus randomly sampled genomic sequences for multiple species |
| motif_enrichment_multi_promotor_seqs | Statistical assessment of motif enrichments in a set of non-random versus randomly sampled gene promotor sequences for multiple species |
| read_blast | Import BLAST output file |
| read_blast_databases | Import BLAST output file |
| sample_chromosome_intervals | Helper function to sample random intervals of length 'interval_width' from chromosomes |