We defined the upstream region of a gene as 1 kb of sequence upstream of the ATG (few UTR sequences are known), or until an annotated gene is encountered on either strand, whichever sequence length is smaller.
The capping regions included the first and last five residues or first and last 25% of total helical length, respectively, whichever was larger.
Only those ESTs that have over 95% identity to the genomic counterpart over half the length of ESTs' length or 50 bp whichever is longer are included.
In cases where two orthologs share MDSs, the length of the shared regions is usually conserved relative to that in Oxytricha (all but 4 are similar within 50 bp or 10%, whichever is larger, of the length of the shared gene segments in Oxytricha).
You can slice whichever way, depending on what length of fry you like.
But the established presence provision is being removed, so all students will need to show they can support themselves for up to nine months or the full length of their course, whichever is shorter.
We use 200 bp or 20% of the original length as the threshold, whichever is greater.
Quality criteria taken were the following: (1) failed sequence reads, (2) sequences with low quality tags, and (3) sequences that are shorter than half the expected amplicon length or 250 bp, whichever the shortest.
Any sequence that contained a low-quality barcode or that failed to be at least half the expected amplicon length (or 250 bp, whichever was shortest) was removed from the data pool.
Loading was stopped at fracture or 106 cycles, whichever occurred first, and microcrack density and length were measured in the loaded region and in a control region that was not loaded.
