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Alignments were manually adjusted and ambiguous regions were excluded from the alignments using Mesquite 2.5 [79].
Sequences were then manually adjusted and aligned to the Greengenes 16S rRNA gene database [66] in ARB [67].
Alignments were subsequently manually adjusted and annotated in BioEdit 7.0.9 where necessary.
Alignments were manually adjusted and DNA sequences reverse aligned to correspond with protein alignments.
Luminal contours were manually adjusted and plaque composition assessed for each frame.
Sequences were aligned using the program MUSCLE (Edgar, 2004 ), manually adjusted and displayed using ALSCRIPT (Barton, 1993 ).
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MicroSuite FIVE software was used to register images, and Fiji software was used to manually adjust and analyze images.
MicroSuite FIVE software was used to fuse images and Adobe Photoshop and Fiji software was used to manually adjust and analyze images.
MicroSuite FIVE software was used to register images, and Adobe Photoshop and Fiji software was used to manually adjust and analyze images.
Sequences were selected based on their similarity and then aligned and manually adjusted using ClustalW and BioEdit.
These were aligned and manually adjusted using ClustalW and BioEdit.
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