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Illumina's alignment tool, ELAND, was used to align the sequence reads to genome build 36 and exon junction databases.
Sequences from S with a BLAST E-value <= 10-10 thethe seed are aligned to the HMM using the align2model software; using HMMs to align the sequence produces somewhat more global alignments than produced by BLAST.
Based upon these results we now provide recommendations to users on the current state of the art for aligning homologous sets of RNAs: 1. Align the sequence set with a (fast) program of your choice.
A sequence (from LyTASK) to profile (from the SAlign templates) alignment was then performed with ClustalW so as to align the sequence of the unknown structure with those of the known structures.
To test sequence-to-structure alignment, we take two homologous proteins of known structure and align the sequence of one (the target) to the structure of the other (the template).
In an attempt to understand how the [Lys]-fullerene might bind to a mammalian Nav channel, we align the sequence of NavAb to Nav1.8.
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Replacing some by the equivalent is a way to align the sequences.
CLUSTAL X software was used to align the sequences (Thompson et al. 1994).
The mismatch kernel, however, does not explicitly align the sequences.
MegAlign (DNASTAR, Madison, WI) was used to align the sequences and generate a consensus sequence.
Gaps due to insertion/deletion events were introduced to align the sequences of the ITS1 and ITS2 regions.
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