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While numerous papers suggest that flexibility could enable one protein to bind to many partners, we might have been the first to suggest that flexibility would provide a means for multiple sequences to bind to a common partner.
For all cleaned PDB chains, secondary structures are computed using DSSP; and non-redundant sequences (defined as kernel) are generated by mapping multiple sequences to one representative (M 1 or many-to-one mapping).
New software includes a faster application-specific pattern-search, a new version (2.0) of the regular expression and Perl search as well as the possibility to load a fasta-format file with multiple sequences to screen for promoter patterns (including tardigrade-specific or general promoter motifs of interest).
Note that compared to these hits (designated TE3), the MER1A transposon in human ANRIL is located closer to the 3′ end of exon 3. To examine the context of the insertion of TE3, we used MEME, a program that detects potential motifs in multiple sequences, to analyse the exon 3 sequences.
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USA. was used to align and edit multiple sequences and to calculated the distance matrices.
When there were multiple sequences mapped to the same gene symbol, the sequence with the largest fold change was assigned to that gene.
The dependence of (T_{ij}) on (tau_{ij}) as reflected in Figure 2 results from accumulating the data from multiple sequences belonging to different ego-alter pairs.
Using the 7 primary proteins, we have carried out multiple sequences alignment to develop scores between sequences.
If multiple sequences pointing to the same TSS were obtained it is more likely that they represented authentic TSSs rather than random mRNA degradation products.
Sequencing traces were analysed using Sequencher software (GeneCodes Corporation, Ann Arbor, MI, USA), and multiple sequences aligned to aid mutation detection.
It has been shown that the 5′-untranslated region (UTR) of UBC24/ PHO2 contains multiple sequences complementary to miR399 [ 22].
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Justyna Jupowicz-Kozak
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