However, none of the four sequence classification methods work well with non-standard sequences, and a modified classification method was deemed necessary.
Otherwise, sequences are classified as non-standard sequences, and result in the particular cases being described as the fourth category "Other (non-standard sequences)".
Because standard sequencing error rates of the Illumina GAII are low (< 0.5%) in the first 20 bases of a read [ 37] we expect that the first six bases in our sequence dataset were affected by non-standard, systematic, sequencing errors.
Owing to the complex nature of the RNA-seq reference genome, taking advantage of PE sequence reads relies on the ability of the mapping algorithm to map 'chimeric' fragments: for example, the first read of a pair may map to a non-standard exon exon junction sequence and the second read to the main spliced transcript.
Among the 219 entries, 197 peptide sequences match the condition to have sequences of size between 10 and 80 residues without non-standard amino acids in their sequence.
For example, BLANNANOTATOR assigns non-standard annotations to bacterial sequences.
In addition, we included one sequence per non-standard exon exon junction (up to three skipped exons, i.e. junctions 1 3, 1 4, 1 5 but not 1 6).
Haarlem/NITR202 contains 2878 genes approximately 90%% of all genes from this strain found in homologous groups composed of non-standard nucleotides, even though this genomic sequence record is deposited in NCBI as a complete genome, a sequence status commonly related to high-quality data.
The method is illustrated with four case studies of pairs of sequences involving non-standard evolutionary events.
However, we could not detect any sequences in non-standard introns sharing similarity with known repetitive elements, participation of duplication-dependent transposons with intron gain therefore remains elusive.
Sequences are checked for the correct length for the locus and the absence of any characters other than A, C, G and T; the submitter is alerted if any entered sequence is of non-standard length or contains unexpected characters.
