The list of putative TEs was manually curated to remove sequences with two LTRs in opposite directions (two instances) and sequences with large (>100 bp) gaps (25 instances).
There's another huge storm, for instance, and a sequence in which the lifeboat is bombarded by wave after wave of flying fish.
For BlastN and MegaBlast, the reads were made non-redundant and given a unique identifier containing the number of instances and the sequence (e.g. 7xACGT…).
For instance, the sequence, and the sequence, for every ; on the other hand, the sequence.
We run them requiring one motif instance per sequence and limiting the search to the primary sequence strand only, while leaving other parameters at their defaults.
Endeavour is another method that relies on the integration of biological evidence resulting from many different kinds of data, for instance, PPIs, pathways, gene expression and sequence similarity (Aerts et al., 2006).
For instance, sequencing and allele specific PCR are both labor-intensive and time consuming due to the manual post-PCR procedures, which lead to the unfavorable turnaround time and latent risk of DNA contamination.
The primers LepF1 and LepR1 [41] were used in most instances, but amplification and sequencing using the 'Lep mini primers' (MLepF1, MLepR1) [42] was necessary for a few older specimens.
In many instances, PCR amplification and sequencing revealed that the 3' ends of coding regions contained short (< 100 bp) introns.
Searching the tammar genomic database [ 25] using tammar IFITM genes yielded one match for each gene, and in each instance this sequence contained an intervening intron.
