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Dot plots compare two sequences by organizing one sequence on the x-axis, and another on the y-axis, of a plot. When the residues of both sequences match at the same location on the plot, a dot is drawn at the corresponding position.
Gene Annotator: The Gene Annotator or GA tool takes as input a list of gene symbols, RGD IDs, GenBank accession numbers, Ensembl identifiers, or a chromosomal region and retrieves gene orthologs, external database identifiers and ontology annotations for the corresponding genes in RGD. The data can be downloaded into an Excel spreadsheet or ...
Ab Initio gene prediction is an intrinsic method based on gene content and signal detection. Because of the inherent expense and difficulty in obtaining extrinsic evidence for many genes, it is also necessary to resort to ab initio gene finding, in which the genomic DNA sequence alone is systematically searched for certain tell-tale signs of protein-coding genes.
The two general steps for constructing a gene co-expression network: calculating co-expression score (e.g. the absolute value of Pearson correlation coefficient) for each pair of genes, and selecting a significance threshold (e.g. correlation > 0.8). The input data for constructing a gene co-expression network is often represented as a matrix.
Two fundamental calculations are central to population genetics: allele frequencies and genotype frequencies. [1] Genotype frequency in a population is the number of individuals with a given genotype divided by the total number of individuals in the population. [ 2 ]
In the context of gene finding, the start-stop definition of an ORF therefore only applies to spliced mRNAs, not genomic DNA, since introns may contain stop codons and/or cause shifts between reading frames. An alternative definition says that an ORF is a sequence that has a length divisible by three and is bounded by stop codons.
Microsoft Excel is a spreadsheet editor developed by Microsoft for Windows, macOS, Android, iOS and iPadOS.It features calculation or computation capabilities, graphing tools, pivot tables, and a macro programming language called Visual Basic for Applications (VBA).
Often, it is more useful to calculate the information content with the background letter frequencies of the sequences you are studying rather than assuming equal probabilities of each letter (e.g., the GC-content of DNA of thermophilic bacteria range from 65.3 to 70.8, [3] thus a motif of ATAT would contain much more information than a motif of ...