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Alignment of the initial physical map with the draft sequence assemblies identified BAC contigs that potentially linked sequence SC (Figure 1).
Compared with other aligners, ELAND is very efficient; however, Eland can map reads using up to the first 32 bases; for longer sequences the bases after 32 willbe mapped sequentially after the alignment of the initial 32.
First, we looked for alignment of the initial Methionine (Met) amino acid to a downstream Met in multiple proteins, which may point to the less common initial Met being an incorrect translation start position.
Multiple alignment of the initial SST isolated messenger RNAs (mRNAs) is presented as a supplementary information (Additional file 2), while the multiple alignment of the corresponding protein sequences showing the similar signal peptides is presented in Figure 1 with the phylogenetic tree of the SST identified family members.
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Indel and dCAPS markers were designed based on the existing sequence alignment of Nipponbare and 93 11, as well as sequence alignments of the initial 62-kb candidate region for dep in Koshihikari and O. glaberrima.
Multiple alignments of the initial cluster members constructed using the MUSCLE program [ 50] were used as PSSMs for a PSI-BLAST search [ 49] against the database of Archaea proteins; significantly similar proteins (domains) were added to the corresponding original clusters.
We also show the alignment error of the initial (not) aligned database (None).
To illustrate the effect of the alignment procedure, histograms of the initial and the final (after alignment) correlation coefficients that were computed between each fingerprint and the target signal are presented in Fig. 2.
Building on the concept of constructive alignment, the initial pool of 12 items focused on the alignment of learning outcomes, teaching and learning activities as well as the assessment implemented within the tertiary engineering curriculum.
The segment (35%) at the top of group F had a dense contiguous alignment spanning the initial 28% of Mt-2.
Class averages of the IP3R were calculated after reference-free alignment using IMAGIC and then refined using the SPIDER alignment routine using class averages of the initial reference-free alignment.
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