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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.
EXACT is based on the perfect phylogeny model, and uses a very fast homotopy algorithm to evaluate the fitness of different trees, and then it brute forces the tree search using GPUs, or multiple CPUs, on the same or on different machines: Brute force search and homotopy algorithm: Jia B., Ray S., Safavi S., Bento J. EzEditor [18]
Many EAs, such as the evolution strategy [10] [11] or the real-coded genetic algorithms, [12] [13] [8] work with real numbers instead of bit strings. This is due to the good experiences that have been made with this type of coding. [8] [14] The value of a real-valued gene can either be changed or redetermined.
Galaxy [2] is a scientific workflow, data integration, [3] [4] and data and analysis persistence and publishing platform that aims to make computational biology and other scientific disciplines accessible to research scientists that do not have computer programming or systems administration experience.
The distance matrix can come from a number of different sources, including measured distance (for example from immunological studies) or morphometric analysis, various pairwise distance formulae (such as euclidean distance) applied to discrete morphological characters, or genetic distance from sequence, restriction fragment, or allozyme data.
The BLAST family of search methods provides a number of algorithms optimized for particular types of queries, such as searching for distantly related sequence matches. BLAST was developed to provide a faster alternative to FASTA without sacrificing much accuracy; like FASTA, BLAST uses a word search of length k , but evaluates only the most ...
Local search with fast k-tuple heuristic, slower but more sensitive than BLAST: Both: GGSEARCH, GLSEARCH Global:Global (GG), Global:Local (GL) alignment with statistics: Protein: Genome Magician Software for ultra fast local DNA sequence motif search and pairwise alignment for NGS data (FASTA, FASTQ). DNA: Hepperle D (www.sequentix.de) 2020 ...