The phrase "alignment cut off" is not standard in written English and may cause confusion.
It could be used in contexts related to design, graphics, or data processing where alignment is interrupted or not completed.
Example: "The alignment cut off at the edge of the page, resulting in a misprint."
Alternatives: "alignment interruption" or "alignment disruption".
The Infernal options for a default search is given in the CM model files provided by Rfam, and depends on the model with the following parameters as variants: -g (global/local(default) alignment), -T (score cut off, set at the so-called gathering score cutoff for the given model), and –fil-no-hmm (turns of HMM pre-filtering, speeding up the search at the cost of sensitivity).
The map was built with a relatively relaxed alignment cut-off value of 1e-21.
The final map was built with a more relaxed alignment cut-off value of 1e-09, followed by removal of entanglements with the DQ-er function at cut-offs of 1e-10 to 1e-12.
The BAC contigs were built with a slightly relaxed alignment cut-off value of 1e-09, which maximised the number of incorporated BACs, but also resulted in a high initial number (11221) of questionable fingerprints, with friction alignment.
On the other hand, setting of high alignment cut-off thresholds (score = 40) resulted in the efficient highlighting of only those coding regions with a significant similarity to sequences in databases, a pool of genes that are easily identified by conventional methods.
An optimal physical map quality, with relatively large contigs containing few questionable clones was obtained with a band size tolerance of 5 (which corresponds to a 0.5 bp size difference in the fingerprints) and an alignment cut-off value of 1e-11.
For the set of restriction sites from step 1, or as provided by the user, all valid upstream, downstream and, if desired, hybridization probe primers within a scan window are enumerated, considering the user-defined parameters for GC-content, melting temperature and self alignment cut-offs.
All known protein sequences from Arabidopsis were individually aligned against the sequences from the entire proteome of Arabidopsis using blastp to select alignments with an E-value cut off of 1x10-20 and which covered 80%% of the query sequence [ 60].
The sequence alignment overlap and the E-value cut off can be preset in accordance with the goal of the experiment [21], [29].
