That is, if we trim sequences to a minimum of 20 colors, the minimum nucleotide length will be 19.
The size ranged from 145 224 nucleotides, with a 6-nucleotide minimum separation size between polymerase chain reaction (PCR) products.
Moreover, most ORF-finding algorithms have historically set 300 nucleotides as the minimum ORF size for gene annotation, which incorrectly classifies genuine proteins corresponded RNA into noncoding RNAs (ncRNAs).
Increased microsatellite frequencies were expected with one allowed mismatch, because the minimum locus size was 15 nucleotides as in perfect microsatellites.
This assembly was run with a minimum match size of 19 nucleotides, match percentage of 93%, mismatch penalty of 18, and gap penalty of 30.
For this assembly, we used a minimum match size of 19 nucleotides, match percentage of 88%, mismatch penalty of 18, and gap penalty of 30.
The assembly was run with a minimum match size of 19 nucleotides, match percentage of 95%, mismatch penalty of 18, and gap penalty of 30 (further information on assembly is available from the authors by request).
Among the pea ESTs, 118 potential SSRs, with more than five repeat units or a minimum repeat size of 20 nucleotides, were identified in 112 contigs of pea with the program SSRIT (Temnykh et al., 2001; Appendix S1).
Open reading frames within the regions of interest identified by SearchDOGS are obtained using GetORF with default parameters [ 17] except that the minimum ORF size is 60 nucleotides (start to stop).
For each pairwise BLAT hit, we obtained a pairwise alignment using bl2seq from BLASTALL (Altschul et al. 1990) and extracted from this alignment the longest ORF (minimum size 300 nucleotides) based on the outgroup sequence.
