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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.
TurboMass is GC/MS software created by PerkinElmer. Universal Mass Calculator Freeware: UMC is programmed as a mass spectrometry tool to assist interpreting measurement results, mainly derived from molecular or quasi-molecular ions. It can be used for the calculation of: Mass deviation (mmu or ppm) of measured mass from given empirical formula
Bio-Synthesis, Inc. (BSI) is a biotechnology company headquartered in Lewisville, Texas.It is a provider of custom and catalog peptides, custom oligos, antibodies, organic synthesis, and analytical services.
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.
Indication of the origin and terminus of DNA replication on a GC skew and cumulative GC skew plot. Richness of G over T in the leading strand, resulting in a GC skew sign at the origin and terminus. GC skew is when the nucleotides guanine and cytosine are over- or under-abundant in a particular region of DNA or RNA. GC skew is also a ...
PCAHIER, [17] another binning algorithm developed by the Georgia Institute of Technology., employs n-mer oligonucleotide frequencies as the features and adopts a hierarchical classifier (PCAHIER) for binning short metagenomic fragments. The principal component analysis was used to reduce the high dimensionality of the feature space.