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One way to visualize the similarity between two protein or nucleic acid sequences is to use a similarity matrix, known as a dot plot. These were introduced by Gibbs and McIntyre in 1970 [1] and are two-dimensional matrices that have the sequences of the proteins being compared along the vertical and horizontal axes.
Gene Set Association Analysis for RNA-Seq GSAASeq are computational methods that assess the differential expression of a pathway/gene set between two biological states based on sequence count data. GeneSCF a real-time based functional enrichment tool with support for multiple organisms.
Here two different gap penalties are applied for opening a gap and for extending a gap. Typically the former is much larger than the latter, e.g. -10 for gap open and -2 for gap extension. This results in fewer gaps in an alignment and residues and gaps are kept together, traits more representative of biological sequences.
This page is a subsection of the list of sequence alignment software. Multiple alignment visualization tools typically serve four purposes: Aid general understanding of large-scale DNA or protein alignments; Visualize alignments for figures and publication; Manually edit and curate automatically generated alignments; Analysis in depth
The concept of gene co-expression networks was first introduced by Butte and Kohane in 1999 as relevance networks. [6] They gathered the measurement data of medical laboratory tests (e.g. hemoglobin level ) for a number of patients and they calculated the Pearson correlation between the results for each pair of tests and the pairs of tests which showed a correlation higher than a certain level ...
Calculate the distance from each of the taxa in the pair to this new node. Calculate the distance from each of the taxa outside of this pair to the new node. Start the algorithm again, replacing the pair of joined neighbors with the new node and using the distances calculated in the previous step.
This list of phylogenetics software is a compilation of computational phylogenetics software used to produce phylogenetic trees. Such tools are commonly used in comparative genomics , cladistics , and bioinformatics .
The plot visualizes the differences between measurements taken in two samples, by transforming the data onto M (log ratio) and A (mean average) scales, then plotting these values. Though originally applied in the context of two channel DNA microarray gene expression data, MA plots are also used to visualise high-throughput sequencing analysis.