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| general:bioseqanalysis:intro [2019/01/21 20:21] – [In silico characterization] ingo | general:bioseqanalysis:intro [2019/01/21 20:22] (current) – [In silico characterization] ingo | ||
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| Basically, in silico analyses of gene function boil down to three general approaches | Basically, in silico analyses of gene function boil down to three general approaches | ||
| * The identification of functionally annotated sequences displaying a significant sequence similarity. The most common tool to do this is [[https:// | * The identification of functionally annotated sequences displaying a significant sequence similarity. The most common tool to do this is [[https:// | ||
| - | * The identification of evolutionary conserved subsequences -sometimes referred to as //domains// - in the sequence of interest. One of the most widely used tools/ | + | * The identification of evolutionary conserved subsequences -sometimes referred to as //domains// - in the sequence of interest. One of the most widely used tools/ |
| * The identification of short motifs in a sequence. Note, contrary to the other two approaches, a motif search typically does not rely on the inference of an evolutionary relationship((Motifs are short sub-sequences of DNA or a protein of defined length, e.g. the start codon //**ATG**// or the canonical splice donor and splice acceptor sites GT-AG. Due to their short length, it is feasible to assume that they can emerge independently more than once in the course of evolution.)) | * The identification of short motifs in a sequence. Note, contrary to the other two approaches, a motif search typically does not rely on the inference of an evolutionary relationship((Motifs are short sub-sequences of DNA or a protein of defined length, e.g. the start codon //**ATG**// or the canonical splice donor and splice acceptor sites GT-AG. Due to their short length, it is feasible to assume that they can emerge independently more than once in the course of evolution.)) | ||
| ===== Integrative approaches ===== | ===== Integrative approaches ===== | ||
| Nowadays, experimental approaches, and those that are computer-based are far from being mutually exclusive. People rarely enter the lab without a prior idea about what a certain gene product could do. And likewise, //in silico// analyses on the computer heavily depend on the amount of existing information that can be exploited in the process annotating the function of an unknown gene product. In essence, annotating a novel gene product is equivalent to connecting it to the network of existing information about gene product function. Information is transferred, | Nowadays, experimental approaches, and those that are computer-based are far from being mutually exclusive. People rarely enter the lab without a prior idea about what a certain gene product could do. And likewise, //in silico// analyses on the computer heavily depend on the amount of existing information that can be exploited in the process annotating the function of an unknown gene product. In essence, annotating a novel gene product is equivalent to connecting it to the network of existing information about gene product function. Information is transferred, | ||