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These family alignments were manually edited in order to ensure the correct alignment of the transmembrane regions, as well as of other OR protein motifs (such as an N-glycosylation site).
To ensure the correct alignment for cross-linking, 2-amino-6-mercaptohexanoic acid was used as the d-amino acid.
In order to obtain alignments of intron-containing genes, we first used sequences for S. cerevisiae, Saccharomyces mikatae, S. kudriavzevii, and S. uvarum to create a seed alignment with mLAGAN (Brudno et al. 2003), and then manually edited it using RALEE (Griffiths-Jones 2005) to ensure the correct alignment of both splice sites and BPs.
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The alignments were manually checked to verify their integrity and to ensure the correct distance (10 20 kb) between mate-paired sequences.
To ensure the correct annotation, probesets from both microarray platforms, as well as MPSS tags, were mapped by sequence alignment to a human transcriptome (HTR) database that was previously used for a multiple platform comparison study [ 20, 21].
Endoscopy reports were obtained to ensure the correct biopsy location.
The ViSQOL error is down to the spectrogram windowing and the correct alignment of patches.
Figure 20(c) indicates the correct alignment of the two range profiles.
It is possible that students in the linear visualization study failed to make the correct alignment.
Likewise, a FN is a pair in the correct alignment not present in the calculated alignment.
We classify each indel in the correct alignment as a TP or a FN based on the predicted alignment.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com