DSL for blastn programs The blastn application searches a nucleotide query against nucleotide subject sequences or a nucleotide database. Four different tasks are supported: 1.) “megablast”, for very similar sequences (e.g, sequencing errors) 2.) “dc-megablast”, typically used for inter-species comparisons 3.) “blastn”, the traditional program used for inter-species comparisons 4.) “blastn-short”, optimized for sequences less than 30 nucleotides.

DSL for blastp programs The blastp application searches a protein sequence against protein subject sequences or a protein database. Three different tasks are supported: 1.) “blastp”, for standard protein-protein comparisons 2.) “blastp-short”, optimized for query sequences shorter than 30 residues 3.) “blastp-fast”, a faster version that uses a larger word-size

DSL for command line parameters that are common to all blast applications

Molecule type of input, values can be nucl or prot

Input file type for makeblastdb

DSL for command line arguments for the NCBI makeblastdb tool

OutputType options Tabular, TabularWithComments, and CSV can be additionally configured to produce a custom format specified by space delimited format specifiers. When not provided, the default value is: 'qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore', which is equivalent to the keyword 'std'

alignment view options