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Thereafter, MEF2 coding sequences were aligned according to the previous alignment of MEF2 protein sequences by ClustalW as implemented in MEGA4 [78].
Briefly, the two longest sequences are first aligned, and shorter sequences are progressively added onto the previous alignment.
The main advantage of the Cα torsion angle criterion is that it does not depend on a previous alignment of the structures, and that the direction of the change is also defined.
From there, NY 43 overlapped US 4 northward to Defreestville, where it rejoined its previous alignment.
It rejoined its previous alignment at I-790's interchange with Genesee Street.
NY 16 was rerouted to follow the new highway for two miles (3 km) before exiting the freeway and returning to its previous alignment.
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Newly aligned SVRs are named aSVR while previous alignments are named simply bSVR.
Trimmed unmapped reads are aligned and used in conjunction with previous alignments to identify chimeric events by examining exon junctions from the annotation file.
Sequences were aligned manually using SE-AL v2.0a11 Carbon [following previous alignments and excluding the third hypervariable region in the case of wsp [ 9, 27, 29]].
Three initial alignments of the amino acid sequence of the TSHR TMD (or the FSHR and LHR TMDs) with the previous alignments of GPCRs homologues were obtained using the program ClustalW.
Improvements were due to re-alignment of segments which were displaced/oriented differently in previous alignments.
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