The phrase "alignments which have" is correct and usable in written English.
It can be used when discussing specific alignments that possess certain characteristics or features.
Example: "The alignments which have been established over the years are crucial for our understanding of the project."
Alternatives: "alignments that possess" or "alignments exhibiting".
Using VISTA's pre-computed human vs. mouse sequence alignments, which have been downloaded into our local server, SNPMiner scans all 100 bp regions encompassing each variant retrieved from dbSNP and identifies the 100 bp region with maximum identity between the mouse and human sequence.
To evaluate the performance of RNAstrand on alignments which have not been identified as structured RNA by RNAz, we constructed a second test set which only consists of alignments not classified as structured RNA by RNAz in both reading directions.
These are serial, and independent pairwise sequence alignments (which has a bearing on the comments below too), each sequence aligned is a read from a genome sequencer, an independent measurement of the sequence, they are not and should not be taken en masse and assessed as an MSA.
For suspicious alignments (which had low percent identities or many gaps), we removed problematic sequences and reran PAML on these revised alignments.
The TPS-TNO was designed and synthesized with in mind to achieve the photo-induced spin alignment which has been observed with anthracene-based radicals [3,4].
This phenomenon is in agreement with the dependence of the photodegradation ability of the TiO2 conduction band with the LUMO level of the adsorbed molecule (band alignment) which has already been observed [10, 12].
If an investigator draws conclusions from an alignment which has not been examined with increased local covariation, there is an increased risk of drawing erroneous conclusions from the alignment.
The first category is based on sequence alignment, which has been reviewed in [ 6].
In the current study, we did not measure knee alignment, which has been shown to be associated with BMLs [ 9].
Second, we did not measure knee alignment, which has been shown to be associated with BMLs [ 3, 9].
