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Exact(10)
After one round of alignment, 'duplicate' subtomograms that had aligned to the same position as another subtomogram were removed, and clearly misaligned particles (those not oriented to the surface of the tube) were excluded by setting a cross correlation threshold for each individual tube.
The first round of alignment was performed using SATé + PRANK, and the second round was performed using SATé + MAFFT.
The most common approach to reference-based genome assembly is a single round of alignment followed by quality filtering and variant detection.
The detected junctions in each sample were pooled as raw junctions for the second round of alignment (default parameters and '--no-novel-juncs').
The particles were subjected to a final round of alignment to eight references in SPIDER and MSA with hierarchical ascendant classification into 150 classes in IMAGIC.
After a given round of alignment, those sequences that most obviously caused regions of problematic alignment were progressively removed until remaining sequences could be aligned without large indels.
Similar(50)
We performed a new round of alignments to identify the coding region (CDS) of each mapped transcript.
The hairpin (precursor) sequences of the cattle miRNAs with mature sequences that showed no more than two mismatches in the previous alignment step were then selected for a second round of alignments against the 57 vertebrate genomes.
When the alignments had stabilized, more than 95% of the images aligned to the same references in consecutive rounds of alignment.
Both rounds of alignment were performed using SATé + MAFFT.
Additional rounds of alignment were conducted with successively lower levels of sequence similarity.
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