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There are two main driving factors to consider here: First, G/C and A/T represent complementary base pairs, as G is always paired with C (and vice versa), while A is always paired with T (and vice versa). Therefore the frequency of G is always equal to C, and the frequency of A is always equal to T. Second, G is paired with C via 3 hydrogen bonds, while A ...


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The frequency of the bases in the genome isn't equal to 0.25, the frequency depends on what kind of organism you mean. However let's take a look at some of them: bacteria, most of the time we can see a bias towards some bases, this could be a GC bias, for example if the bacteria lives in extreme conditions, because GC can vorm three hydrogen bonds compared ...


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My experience is with Affymetrix probes for Drosophila, not H.sapiens, and only with one version. Nevertheless I'll describe the situation I encountered in case it is relevant to yours. Apologies if it is a red herring. What I did with the Affymetrix data sheet was use it to construct my own SQL relational database containing probesetIDs and geneIDs (as ...


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Answer You can't. Clustal doesn't provide the options of setting the sort of restraints you would like. Multiple Sequence Alignment (MSA) is difficult to program and the authors of Clustal have been refining their algorithm for years. If it were perfect and completely robust they might be in a position to add more user tweaking, but at the moment you're ...


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Let me begin in the sample preparation to explain you the index primers.... and let me assume please that you want to sequence amplicons like 16S. Let me further assume that you have 96 samples, which means that you have one complete PCR plate full of samples. First you prepare your samples. You are doing a amplicon PCR, clean that PCR, attach the adapters ...


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You're not wrong but gap can mean more than that. A good recent reference is this paper: Genetic variation and the de novo assembly of human genomes. Essentially, a gap occurs if something happens in our genome that can't be explained by uniformity. Since our genome is highly complicated, you can expect gap is also more than just mis-sequencing. The gap you ...


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The word ‘gap’ can be used both loosely and in specific genomic contexts, as listed by @Student T. The usage that seems to relate to your question — Sequence Coverage Gaps — is quite nicely illustrated in the Wikipedia entry on ‘Contig’. I reproduce, below, a modified form of a (public domain) illustration from it. The sequences of the ‘contigs’ (see ...


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I'm restricting this answer to Illumina. Even then, I don't know about the exact details of the raw data analysis (it is a proprietary software). Basically Illumina records the sequence based on photographic images. Each nucleotide has a distinct fluorescent label. In a cycle, a nucleotide is pumped and unincorporated nucleotides are washed off (this is ...


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"To me it seems like both clone based sequencing and shotgun sequencing could have been used together," I believe they were. The public project cut up the genome into BACs and shotgunned every BAC, and then put the BACs together, while Venter used some sequence position information from the public effort to help him place his shotgun pieces. ...



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