Therefore, reads that aligned to the MAC were sorted into three categories of mapping specificity: reads fully aligned to the MAC (50,057), reads with some internal discontinuity or mismatch that could have resulted from cloned DNA rearrangement (27,002), and reads aligned to the MAC from one end only with a nonmapping >10 bp terminal extension at the other end (12,037; File S1).
For standard gDNA we found no significant difference in the sequence performance among the samples tested on the short-read ABI SOLiD platform: The sequence specificity (reads on target) was ~65%, the uniformity was ~85%, and the genotype concordance was 99%.
The main inspiration to overcome this hurdle came from understanding how naturally occurring sequence-specific DNA-binding proteins achieve their specificity in reading double-stranded DNA and then using these principles to generate custom enzymes.
That is, loss of specificity of reading.
Thank you for choosing to send your work entitled "Membrane immersion allows rhomboid proteases to achieve specificity by reading transmembrane segment dynamics" for consideration at eLife.
He brushes them off with phrases like, "That was the responsibility of the delegate"; "I cannot speak with any specificity"; "I read the memo; I presume it must have registered with me"; and "I am not a psychiatrist".
However, standard RNA-seq library generation protocols do not preserve strand specificity, as reads synthesized from the first-strand cDNA cannot be distinguished from the second strand (23 26).
To increase the accuracy and specificity of read mapping and mutation identification, several pre-processing filters were applied to the raw sequencing tags.
To generate a measurement of the specificity of reads that were found to align to gene models, we generated a synthetic set of reads that were the reverse, but not the reverse compliment, of all observed sequences reads (entire dataset).
Our analyses indicate that rhomboid proteases achieve substrate specificity first through reading TM dynamics, which endows them with different properties relative to soluble proteases.
