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Newly identified homologues were realigned to the model using cmalign from INFERNAL 1.0.
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Clusters of transcripts that mapped to overlapping genomic regions were realigned to the genome using the program GeneSeqer [ 47] which has specific splice-site models for each species.
Aligned reads were realigned to the genome.
The functional images were spatially realigned to the mean image.
The routes were realigned to the bypass between 1976 and 1989.
The remaining functional images were realigned to the first scan to correct for head movement.
All volumes were realigned to the first volume to correct for head movements between scans.
Scans were realigned to the first EPI image.
Regions containing indels were then realigned to the reference genome.
To correct for motion artifacts, images were realigned to the 11th volume.
NAC frames x+1... N are realigned to the sum of the first x NAC frames.
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