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DNA sequence alignment of unrestricted size in single or multiple GPUs Nucleotide: Local, SemiGlobal, Global: E. Sandes [20] [21] [22] 2011-2015 DNADot Web-based dot-plot tool: Nucleotide: Global: R. Bowen: 1998 DOTLET Java-based dot-plot tool: Both: Global: M. Pagni and T. Junier: 1998 FEAST Posterior based local extension with descriptive ...
An alternative to BLAST for comparing two banks of sequences is PLAST. PLAST provides a high-performance general purpose bank to bank sequence similarity search tool relying on the PLAST [24] and ORIS [25] algorithms. Results of PLAST are very similar to BLAST, but PLAST is significantly faster and capable of comparing large sets of sequences ...
The main diagonal represents the sequence's alignment with itself; lines off the main diagonal represent similar or repetitive patterns within the sequence. In bioinformatics a dot plot is a graphical method for comparing two biological sequences and identifying regions of close similarity after sequence alignment. It is a type of recurrence plot.
The first method requires single perfect matches between the query and database sequences i.e. the two k-mer words are exactly the same. This approach is not considered the most practical. This is because a small k-mer size is necessary in order to achieve high levels of sensitivity, but this increases the number of false positive hits, thus ...
The fourth is a great example of how interactive graphical tools enable a worker involved in sequence analysis to conveniently execute a variety if different computational tools to explore an alignment's phylogenetic implications; or, to predict the structure and functional properties of a specific sequence, e.g., comparative modelling.
This method requires constructing the n-dimensional equivalent of the sequence matrix formed from two sequences, where n is the number of sequences in the query. Standard dynamic programming is first used on all pairs of query sequences and then the "alignment space" is filled in by considering possible matches or gaps at intermediate positions ...
It detects homology by comparing a profile-HMM (a Hidden Markov model constructed explicitly for a particular search) to either a single sequence or a database of sequences. Sequences that score significantly better to the profile-HMM compared to a null model are considered to be homologous to the sequences that were used to construct the ...
MNHN-Tree-Tools is an opensource phylogenetics inference software working on nucleic and protein sequences. Clustering of DNA or protein sequences and phylogenetic tree inference from a set of sequences. At the core it employs a distance-density based approach. Thomas Haschka, Loïc Ponger, Christophe Escudé and Julien Mozziconacci [28 ...