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Additional annotation of MITE01 included prediction of putative primary sequence and secondary structure features consistent with other Helitron-like TEs from Lepidoptera using methods described previously [ 13, 16] using the Mfold DNA server [ 55] (http://mfold.rna.albany.edu/?q=mfold/dna-folding-form).
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The single stranded DNA can server as a facile mediator that place the Ag@Au ACS in proximity of CdS QDs, stimulating the interparticle exciton plasmon interactions between Ag@Au ACS and CdS QDs and thus quenching the excitonic states in the latter.
The Zuker/Turner mfold program (http://mfold.bioinfo.rpi.edu/cgi-bin/rna-form1.cgi) was used to model RNA sequences and the DNA mfold server (http://mfold.bioinfo.rpi.edu/cgi-bin/dna-form1.cgi) was used for DNA secondary structure modeling [24], [25].
In other words, BioBarcode is a bioinformatics template or platform rather than a specific DNA barcode server.
The Mfold DNA web server was used to predict the secondary structure with the following conditions: 25°C, 100 mM Na+, and 2 mM Mg2+ [ 26].
The DNA mfold server (http://mfold.bioinfo.rpi.edu/cgi-bin/dna-form1.cgi; [ 34]) was used to search for stem-loop structures, and the MEME server (http://meme.sdsc.edu/meme4_4_0/intro.html) was used to search for sequence motifs that might be associated with inversions.
The hairpin was calculated to be stable at 60°C in the context of the entire OCP using the DNA folding server at Michael Zucker's website OCP sequence was chosen such that the hairpin was the only stable structure in the OCP, with a ΔG of -0.5 to -1.5 kcal/mol.
Prediction of secondary structure for legitimate tRNAs and their Numts which had the complete tRNA sequence were obtained using the DNA mfold web server [ 36].
All the alignments were obtained via CLUSTALW DNA sequences from NPS@ server (http://npsa-pbil.ibcp.fr).ibcp.fr
The purpose of BioBarcode is to be used by biologists who have specific species information and want to build a DNA barcode database and server.
One sequence, which appeared twice among these aptamers, was designated as A10-2 and subjected to secondary structure prediction using the mFold software [ 15] at 37°C in 150 mM [Na+] and 1 mM [Mg++], a web-based server for DNA folding and hybridization predicting (http://unafold.rna.albany.edu/?q=mfold/DNA-Folding-Form).
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