In the first step (i.e., the Tokenizer step), the text in BP is split into a sequence of words (or tokens).
All IUM reads longer than 60 bp are split into three equal segments, because too short and too many segments lead to inaccuracy of our filter result.
To generate dual AAV vector plasmids, the EGFP CDS (720 bp) was split into two constructs: one containing the N-terminal CDS (PMID: 9759496, bp 1-393) and the other containing the C-terminal CDS (PMID: 9759496, bp 394-720).
The complete genome of K. pneumoniae isolate Kp13 consists of 5,739,888 bp of which 5,307,003 bp form a single, circular chromosome and 432,885 bp are split into six plasmids which range in size from 2,459 bp (pKP13a) to 294,493 bp (pKP13f) (Table 1).
After removal of multiple-aligned reads, unmapped 70-bp reads were split into two 35-nt fragments.
This resulted in alignments with a maximum length of 200 bps (longer alignments were split into overlapping windows of 120 bps with a step size of 40) and a minimum number of aligned sequences (>50% identity) from at least 4 different species.
To use large contigs (≥ 2,000 bp) as input for TGICL, they were split into 2,000 bp-fragments which overlap by 300 bp.
Genomic regions ± 25 kb of any gene were split into 1000 bp bins and transcription-factor-binding sites per bin were represented as a binary matrix (Martello et al., 2012 ).
The resultant sequences were split into one of the two lengths, 201 bp and 401 bp, to generate two large datasets of DNase accessible sequences to be used as a source of background sequences in later analyses.
