The phrase "alignments at the same" is not correct in English and does not convey a clear meaning.
It seems to be an incomplete thought and lacks context to determine its intended use.
Example: "We need to ensure that all alignments at the same level are properly adjusted."
Alternatives: "alignments at the same level" or "alignments in unison".
Rather, we only wish to highlight that the HMMER3 local alignments do have a general tendency towards more significant E-values than HMMER2 glocal alignments at the same false-positive rate (see Fig. 5).
As long as the sum of the consensus threshold and the specificity threshold is lower than one, a position can be in the consensus and specific to one of the alignments at the same time (Supplementary Material at http://www.mrc-lmb.cam.ac.uk/genomes/spial/help.html).ac.uk/genomes/spial/help.html
In short, unlike the alignment results from tools such as BLAST which will generate two distinct partial alignments for a split-read covering a large deletion event, the alignment results of BLAT can directly reveal the deletion event and its up- and down-stream alignments at the same time.
In this approach, reducing the size of each data chunk reduces the size of the mapper job, T alignment, but at the same time more chunks have to be simultaneously sent over the network, which increases the communication time, T comm.
For both sources of variants we applied stringent filter criteria to reduce false calls: (1) genome variants had to appear in at least 40 strains with a minor allele count of at least 5 strains, (2) RNA-Seq variants had to be confirmed by at least 2 alignments within the same strain and had to have less than factor 2 many non-confirming alignments within the same strain.
As discussed earlier, the respective false-positive rates associated to any overlapping HMMER2 and HMMER3 sequence-to-domain alignments can vary greatly at the same E-value cutoff.
If there are multiple alignments with the same alignment score, a single result is selected at random.
Both alignments gave the same tree topologies.
When two alignments had the same coverage, we selected the alignment with the higher score.
We used BWA for non-allele-aware alignments with the same alignment parameters as GSNAP.
B. Amino acid sequence alignments among the same three sequences.
