https://bioinformaticsonline.com/snippets/view/43405/blastpgp-arguments? https://bioinformaticsonline.com/snippets/view/43405/blastpgp-arguments Tue, 28 Sep 2021 05:30:02 -0500 https://bioinformaticsonline.com/snippets/view/43405/blastpgp-arguments blastpgp arguments: -d Database [String] default = nr -i Query File [File In] default = stdin -A Multiple Hits window size (zero for single hit algorithm) [Integer] default = 40 -f Threshold for extending hits [Integer] default = 0 -e Expectation value (E) [Real] default = 10.0 -m alignment view options: 0 = pairwise, 1 = query-anchored showing identities, 2 = query-anchored no identities, 3 = flat query-anchored, show identities, 4 = flat query-anchored, no identities, 5 = query-anchored no identities and blunt ends, 6 = flat query-anchored, no identities and blunt ends, 7 = XML Blast output, 8 = Tabular output, 9 = Tabular output with comments [Integer] default = 0 -o Output File for Alignment [File Out] Optional default = stdout -y Dropoff (X) for blast extensions in bits (default if zero) [Real] default = 7.0 -P 0 for multiple hits 1-pass, 1 for single hit 1-pass, 2 for 2-pass [Integer] default = 0 -F Filter query sequence with SEG [String] default = F -G Cost to open a gap [Integer] default = 11 -E Cost to extend a gap [Integer] default = 1 -X X dropoff value for gapped alignment (in bits) [Integer] default = 15 -N Number of bits to trigger gapping [Real] default = 22.0 -g Gapped [T/F] default = T -S Start of required region in query [Integer] default = 1 -H End of required region in query (-1 indicates end of query) [Integer] default = -1 -a Number of processors to use [Integer] default = 1 -I Show GI's in deflines [T/F] default = F -h e-value threshold for inclusion in multipass model [Real] default = 0.005 -c Constant in pseudocounts for multipass version [Integer] default = 9 -j Maximum number of passes to use in multipass version [Integer] default = 1 -J Believe the query defline [T/F] default = F -Z X dropoff value for final gapped alignment (in bits) [Integer] default = 25 -O SeqAlign file ('Believe the query defline' must be TRUE) [File Out] Optional -M Matrix [String] default = BLOSUM62 -v Number of database sequences to show one-line descriptions for (V) [Integer] default = 500 -b Number of database sequence to show alignments for (B) [Integer] default = 250 -C Output File for PSI-BLAST Checkpointing [File Out] Optional -R Input File for PSI-BLAST Restart [File In] Optional -W Word size, default if zero [Integer] default = 0 -z Effective length of the database (use zero for the real size) [Real] default = 0 -K Number of best hits from a region to keep [Integer] default = 0 -s Compute locally optimal Smith-Waterman alignments [T/F] default = F -Y Effective length of the search space (use zero for the real size) [Real] default = 0 -p program option for PHI-BLAST [String] default = blastpgp -k Hit File for PHI-BLAST [File In] default = hit_file -T Produce HTML output [T/F] default = F -Q Output File for PSI-BLAST Matrix in ASCII [File Out] Optional -B Input Alignment File for PSI-BLAST Restart [File In] Optional -l Restrict search of database to list of GI's [String] Optional -U Use lower case filtering of FASTA sequence [T/F] Optional default = F -t Use composition based statistics [T/F] default = T -L Cost to decline alignment (disabled when 0) [Integer] default = 0]]> Surabhi Chaudhary