This function takes a vector of sequences in FASTA style as input and applies BLAST running on a local blast database. By default, the parameters are configured for blasting small RNA sequences of strand-specific RNA-seq experiments with 100% identity over the whole query sequence.
runBlast(blast_exec, blast_db, ncores, sig_sequences, strand = "plus", identity = 100, dust = "no", soft_masking = "false")
| blast_exec | Path to your installation of the 'blastn' binary |
|---|---|
| blast_db | Path to your local BLAST database |
| ncores | Number of cores used by BLAST |
| sig_sequences | Vector of sequences in FASTA style generated by the sequencesAsFasta |
| strand | Query strand orientation to search against database. By default 'plus', assuming underlying strand-specific RNA-seq experiments. |
| identity | Identity cutoff applied for filtering BLAST results. By default 100%, to find only exact matches over the whole length of the query sequence. |
| dust | The parameter specifies whether low complexity filtering is applied to the query sequence. By default 'no', to prevent false-negative annotations of sequences of interest. |
| soft_masking | The parameter specifies whether low complexity filter is applied to the database. By default 'no', to prevent false-negative annotations of sequences of interest. |
Each row of the resulting data frame corresponds to a BLAST hit including the columns 'qseqid', 'qlen', 'pident', 'length', 'mismatch', 'gapopen', 'qstart', 'qend', 'sstart', 'send', 'evalue' and 'bitscore'.