Sentence examples for minimal alignment length from inspiring English sources

Furthermore, minimal alignment length (hsp filter) was set to 33 to avoid hits with matching region smaller than 100 nucleotides.

First, a blastx search [221] in the NCBI nr.aa database was performed, and all sequences producing an E-value<1E-3 and a minimal alignment length of 33 residues were considered a hit.

Program parameters were varied in repeated runs: CYNTENATOR gap and mismatch penalty parameters were set to 0.1, 0.5, 1, 2, 3, 5, 20, the alignment score threshold was set to 1, the minimal alignment length to 2, the maximal number of retained alignments to 1,000 and the gene coverage filter to 4. MCMuSeC was run to report gene clusters, which are shared by at least two genomes.

Alignment candidate threshold (minimal alignment length to map the read) was optimized with hash size 20.

BLAST (balstn) was used with the default options, with an exception that the minimal alignment length was set to 7 bp.

Our algorithm employed 2 quality assurance criteria for reference sequences identified in BLASTn analysis: minimal alignment length of 98% and annotation as a validly described bacterial taxon (28 ).

We required the minimal length coverage threshold to be 0.7, which means that the minimum alignment length should cover at least 70% of full length of the shortest member in a group of sequences.

† = maximum e-value of 1x10-5, minimum alignment length ~100.

A minimum alignment length l A,min of 20 nt is used for finding pairwise alignments.

Individual alignments were parsed by minimum alignment length and concatenated using FasConcat [ 75] for generation of super alignments.

The sequencing reads for each run were mapped separately using Blast (Blastall v2.2.20) with the following parameters [-p blastn -e 0.0001 -b 20 -v 20 -m 0 –W 11 -F F], allowing up to 6 alignment errors, and minimal alignment lengths of 27 and 30 bp for the 33 and 38 bp long sequencing reads, respectively.