The program also removes sequences with "AAAA", "TTTT", "GGGG", "CCCC", "TGGC" motifs from siRNA efficient candidates.
In step 5, a noise level cutoff removes sequences that occur "noise-level" or fewer times.
This pipeline removes sequences with plasmid similarity, polyA/polyT regions, low base quality and slippage signals.
All unique sequences were filtered to remove sequence copies and only keep sequences with at least 300 bp.
To our knowledge, DeconSeq is the first program optimized to automatically identify and remove sequence contamination from large sequence datasets.
UniRef100 is computed without the overlap threshold in order to remove sequence redundancy resulting from subfragments.
A total of 5.2 × 107 bases from 15,560 cleaned (redundancy removed) sequence documents were analyzed.
The remaining singletons were mapped to contigs in order to remove sequence redundancy.
For coverage-adjusted comparisons, we randomly removed sequence reads from the original alignments.
To remove sequence repeats arising from overlapping transcript variants, the FASTA sequences were assembled into contiguous sequences with CAP3.
