BlastN 2.2.1 Search DBs for Nucleotide Sequence similarity Altschul, Madden, Schaeffer, Zhang, Miller, Lipman Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaeffer,Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), Gapped BLAST and PSI-BLAST: a new generation of protein database search programs, Nucleic Acids Res. 25:3389-3402. Nucleic Acid Sequence blastn blast_init perl " " -10 scheduler_conf 3 scheduler.conf perl "node_exclusive=1\\n" . "nodes=1\\n" . "threads_per_process=16\\n" query Sequence File perl "blast_wrapper -query query.fasta" query.fasta 3 blast2 perl "-out blast_output.txt" 9 blastn compares a nucleotide query sequence against a nucleotide sequence database num_threads perl "-num_threads 16" 6 runtime 1 scheduler.conf Maximum Hours to Run (up to 168 hours) 0.5 The maximum hours to run must be less than 168 perl $runtime > 168.0 The maximum hours to run must be greater than 0.05 perl $runtime < 0.05 perl "runhours=$value\\n" The job will run on 16 processors as configured. If it runs for the entire configured time, it will consume 16 x $runtime cpu hours perl defined $nucleotid_db Estimate the maximum time your job will need to run. We recommend testimg initially with a < 0.5hr test run because Jobs set for 0.5 h or less depedendably run immediately in the "debug" queue. Once you are sure the configuration is correct, you then increase the time. The reason is that jobs > 0.5 h are submitted to the "normal" queue, where jobs configured for 1 or a few hours times may run sooner than jobs configured for the full 168 hours. use_epa This search is for Evolutionary placement perl "" nucleotid_db nucleotide db perl "-db /projects/ps-ngbt/databases/blast/blast_ref_dbs/$value.expt" 4 5_8S its nuclsu nucssu mitssu rpb1 rpb2 UNITE_public_tbas unaligned_its unaligned_lsu unaligned_its_lsu unaligned_ssu unaligned_mitssu unaligned_rpb1 unaligned_rpb2 Sorry, unaligned databases are not valid for EPA perl $use_epa && ($value eq "unaligned_its" || $value eq "unaligned_lsu" || $value eq "unaligned_ssu" || $value eq "unaligned_mitssu" || $value eq "unaligned_rpb1" || $value eq "unaligend_rpb2") Please select a database perl !defined $nucleotid_db choose a nucleotide db for blastn, tblastn or tblastx gap_open_penalty Cost to open a gap (-gapopen; default=5) perl (defined $value)? " -gapopen $value":"" 5 for blastn default=5 4 gap_extend_penalty Cost to extend a gap (-gapextend; default=2) perl (defined $value)? " -gapextend $value":"" 2 5 for blastn default=2; for blastp, blastx and tblastn default=1 Limited values for gap existence and extension are supported for these three programs. Some supported and suggested values are: Existence Extension 10 1 10 2 11 1 8 2 9 2 (source: NCBI Blast page) all_results *