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To identify biologically relevant matches, length of the segment of a query sequence aligned with the matching target in the database was calculated as per cent of the query length as well as the alignment length in bases.
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Bamboo Cut a pipecleaner to match length of bamboo, fold over ends.
Regarding the match length of the SNP-containing reads, more than 80% have a full length match (32 bp), and most of the reads have a match length of 25 or more.
A minimum match length of 30 bp was used for this analysis.
A custom Perl script was used to calculate the percent match length of the protein with the best hit.
japonica with the match length of the paralogous gene pair more than 100 bp and mismatch length/(mismatch length + match length) less than 0.1.
BLAST hits were parsed from output files using tcl_blast_parser_123_V017.tcl [55] with a cut-off of 40% match, 1e-20 normalize-valuelue, and a minimum match length of 30 residues.
Loci with a minimal match length of 40 nt were investigated for a hairpin with approximately the same length of the original rat pre-miRNA.
The ORFs aligned against ORFs with high alignment lengths (match length of at least 50 amino acid) and high identities (≥60%) were listed as potential paralogous ORFs.
A BLASTP [ 108] e-value of 1e 10-5 and percent match length of 50% were used as cut-offs in orthoMCL [ 40] analysis.
In BlastX analysis, a cutoff value of 1 × 10-5 and a minimum match length of 300 bp were used as the similarity threshold.
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