The approach uses the parameters: word frequency, query length and entity matching for distinguishing the user's query into exploratory, targeted and analysis search.
The cDNA and genomic sequences were used in BLASTn searches using both default parameters (word size = 11, expect threshold = 10, match = 2, mismatch = −3, gap existence = −5, gap extension = −2, filter and mask on) and with altered parameters (word size = 7, filter and mask off).
Specifically, we used tblastn (protein query and DNA database) with the default search parameters (word size = 3, BLOSUM62 matrix, gap insertion/extension = 9/2, using the ENSEMBL BLAST interface, these parameters are closest to the "distant homologies" or "no optimisation" search) and found the mammalian hits to have significance scores (P-values) better than about 10E-9.
For initial searches, the default parameters (word size 11 and 1 hit per isolate) were used.
For initial searches, the default parameters (word size 11, 1 hit per isolate and 5000 bp flanking length) were used.
However, changing the BLASTN run parameters (word size reduced to 7, e-value 1E-03) resulted in mapping 65% of the contigs.
Assembly proceeded using the following parameters: word size of 24, bubble size of 50, and minimum contig size of 150 bases.
BLAST searches were done using low stringent parameters (word size at seven, e-value cut-off at 10) against miRBase and non-redundant GenBank sequences.
Protein-coding genes were independently evaluated by searching all open reading frames (ORFs) >80 AA against the nonredundant protein sequence database using BLASTP with relaxed parameters (word size = 2, matrix = BLOSUM45, e-value = 100).
Assembly of J. osense plastome was performed using CLC Genomics Workbench v. 5.5 with following parameters: word size = 22, bubble size = 50, mismatch cost = 2, insertion cost = 3, deletion cost = 3, minimal contig length = 1,000 bp.
Complete genome sequences of 627 mycobacteriophages were concatenated into a single file which was compared with itself using Gepard (Krumsiek et al., 2007 ) and displayed as a dotplot using default parameters (word length, 10).
