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And now, as the field changes generational hands, it's crucial to bring both streams into alignment, to start looking again for the new in the traditional (it's there), and to start locating links to the past in the new (also there).
So you had to figure out how to lay them down in perfect alignment to start with.
The sequence of these DArT markers plus SNP and EST-SSR markers was then used to form a bridge to the sorghum genomic sequence by BLAST alignment to start to unravel the complex genomic architecture of sugarcane.
Local RNA secondary structural alignment has been implemented by allowing an alignment to start or end at any internal node in the tree (Backofen and Will, 2004; Eddy, 2002; Klein and Eddy, 2003), much as local primary sequence alignment allows starting and ending at any residue in the linear sequence.
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The quality of the alignments was filtered according to the following criteria: 1) the minimum match length was set to 29 nucleotides with no gap larger than 1 nucleotide 2) alignments had to start with the DpnII site as the first nucleotides.
We decided that sequences should be complete and typical from the PEXEL motif (Plasmodium Export Element motif) [ 16, 17] to the C-terminal transmembrane domain; the alignments were constrained to start at this motif as well.
Click on the 'Align' button in order to start the alignment process.
The OrthoMCL program [ 62] was used to cluster SEO proteins into subgroups, with an inflation parameter of 3. The protein sequences were aligned with T-Coffee [ 63] and the alignment was end trimmed to start and end with the domains predicted for all SEO proteins (SEO-NTD and SEO-CTD).
However, player alignment start position was set to start of the read, regardless of whether a read was soft clipped or not.
To start an alignment procedure, at least two isolates and one segment must be selected from a 'Browse' result table.
Local alignments will therefore be forced to start and end with consensus match positions (just as in standard Smith/Waterman local sequence alignment).
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