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GC content is found to be variable with different organisms, the process of which is envisaged to be contributed to by variation in selection, mutational bias, and biased recombination-associated DNA repair. [19] The average GC-content in human genomes ranges from 35% to 60% across 100-Kb fragments, with a mean of 41%. [20]
Many sources of bias were already reported – GC content and PCR enrichment, [18] [19] rRNA depletion, [20] errors produced during sequencing, [21] priming of reverse transcription caused by random hexamers. [22] Different tools were developed to attempt to solve each of the detected errors.
OLIGO Primer Analysis Software is a software for DNA primer design. [1] [2] The first paper describing this software was published in 1989. [3] The program is a real time PCR primer and probe search and analysis tool. It additionally performs siRNA and molecular beacon searches, open reading frame analysis, and restriction enzyme analysis.
Oligo Design and Analysis Tools - Oligo calculator and analyzer, antisense design, dilution, resuspension. Protein Hydroplotter - Distinguishes Protein Hydrophilic and Hydrophobic Regions Website
The energy required to break the base-base hydrogen bonding between two strands of DNA is dependent on their length, GC content and their complementarity. By heating a reaction-mixture that contains double-stranded DNA sequences and measuring dissociation against temperature, these attributes can be inferred.
Efficiency involves taking into account such factors as GC-content, efficiency of binding, complementarity, secondary structure, and annealing and melting point (Tm). Primer selectivity requires that the primer pairs not fortuitously bind to random sites other than the target of interest, nor should the primer pairs bind to conserved regions of ...
The information content of an organism is recorded in the DNA of its genome and expressed through transcription. Here, mRNA serves as a transient intermediary molecule in the information network, whilst non-coding RNAs perform additional diverse functions. A transcriptome captures a snapshot in time of the total transcripts present in a cell ...
Chargaff's second rule appears to be the consequence of a more complex parity rule: within a single strand of DNA any oligonucleotide (k-mer or n-gram; length ≤ 10) is present in equal numbers to its reverse complementary nucleotide. Because of the computational requirements this has not been verified in all genomes for all oligonucleotides.