Sentence examples for before being aligned using from inspiring English sources
Accession numbers can be found in Additional File 9. Sequences were formatted in BBEdit Lite 6.1 [ 85] before being aligned using clustalx [ 86] with reduced gap penalties (for pairwise alignments the gap opening penalty was set to 5 and the gap extension penalty to 0.05; for the multiple alignment the gap opening penalty was set to 5 and the gap extension penalty to 0.1).
Complete protein sequences were assembled and labelled in BioEdit [ 43] before being aligned using ClustalX [ 44].
Residues 1-43aa of lactate dehydrogenase from P. vivax (AEP83563.1), P. ovale (AAS77571.1), P. malariae (AAS77572.1), P. falciparum (ABH03417.1), P. berguie (AY437808.1), P. knowles (JF958130.1) and P. yoelli (XP_724101.1) were downloaded from the NCBI protein databases and then edited manually before being aligned using Clustal W2.
Duplicate hits were manually removed before sequences were aligned using M-Coffee [ 110], combining the results of alignments using Muscle [ 111], Mafft [ 112], ProbCons [ 113], PCMA [ 114], and Fsa [ 115].
Images taken before and after photoactivation were aligned using a subpixel registration algorithm (Guizar-Sicairos et al., 2008) and correlation between registered images.
The segments were aligned using BioEdit before they were entered into WebLogo.
The adaptor sequences were filtered out before the subsequent analysis and the resulting reads were aligned using Bismark software [ 57].
In brief, the predicted amino acid sequences of BnaCBLs or BnaCIPKs were aligned using ClustalX1.83 program with the same multiple alignment parameter settings as before.
The tilt series were aligned using MarkerAuto (Han et al., 2015) before reconstruction using IMOD (Kremer et al., 1996).
The resulting refined HMM profiles were aligned using the same parameters as described above before being used for final genomic scans.
Before spike sorting, the artifact waveforms were removed and the spike waveform minima were aligned using the Offline Sorter 2.8 software (http://www.plexon.com, Dallas, TX).
