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Thus, selection of probes for uniqueness within a specified sequence set by the Probe Weaver software requires at least 15°C difference in Tm to the closest hit/s for nontarget sequences in the set.
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IMEx-level curation requires the mapping of binding regions, point mutations and post-translational modifications to a specified sequence within a reference protein sequence database, UniProtKB in the case of IntAct.
Thus, we showed that HIV-1 integration favors a specified sequence at least.
The results page lists all SAASs found within the specified sequence and their functional effect predictions, wild-type/mutant conservation scores, information on disease (human only), experimentally derived functional/structural consequences, changes in position biochemical properties, per-variant validation status and average heterozygosity.
In this paper, we consider the problem of exhaustive counting and discovery of pairs of subwords that co-occur more frequently than expected within a specified distance in a sequence.
This software tool looks for the specific sequences within a specified distance to the 5′ and the 3′ end of the reads.
For each protein sequence, all subsequences within a specified length and mass range are generated.
These sequences include the minimum free energy sequence, as well as all amino acid sequences whose free energy lies within a specified window from the minimum.
Oligonucleotide probes for microarray analysis of gene expression were designed with CombiMatrix probe design software (Probe Weaver) based on: (i) uniqueness within a defined gene and sequence set; (ii) Tm and length within a specified range; 70 75°C, and 35 40-mer 35 40-mervely; and (iii) absence of stable secondarespectivelys and repeat sequences.
Briefly, LTR_STRUC works by sliding a window along genomic sequence and looking for direct repeats that are spaced apart within a specified size range (e.g. 5 10 kb).
Furthermore, training sequences are also used to extract over-represented 6-mer nucleotides within a specified window size around the TSSs, which comprise the so-called positive set.
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