We present the general design principles that overcome the challenges of maximizing optical trap resolution while maintaining single-molecule fluorescence sensitivity, and provide details on the construction and alignment of the instrument.
Sequence construction and alignment was performed using Vector NTI (Invitrogen, Carlsbad, CA).
We conduct GO term analysis for genes collected by the HB network alignment method (please refer to our previous study [ 11] for details on HB network construction and alignment).
TGA-like protein sequences retrieved from GenBank used for phylogram construction and sequence alignment.
With good precision in system construction and careful alignment, the overall nonlinearity can be less than 1%.
2457T, and Yersinia enterocolitica subsp. enterocolitica WA-314, and the amino acid sequences of these homologs, along with that for YcgC from E. coli K12 W3110, were then subjected to phylogenetic tree construction and sequence alignment using LaserGene (DNAstar Inc. Madison, WI).
(PPTX 1221 kb) Additional file 4: PhyML trees (Newick format), trimmed alignments used for phylogenetic tree construction, and original alignments for MCP, ATPase and pDNAP.
HMM construction, searches, and alignments were conducted using HMMER (2.3.2) (Eddy, 1998).
All samples were included and batch processed using a zoom scan filter, three steps peak detector (local maxima mass detection, score connector chromatogram construction, Savitzky-Golay peak recognition) and alignment join aligner.
AD participated in the study design, sand fly rearing, dissections, cDNA library construction and annotation, sequence alignment, phylogenetic analysis, quantitative PCR and drafting the manuscript.
JH participated in the cDNA library construction and annotation, sequence alignment and phylogenetic analysis, immunization of mice by sand flies and the detection of humoral response to sand fly saliva, and drafting the manuscript.
