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In bioinformatics, BLAST (basic local alignment search tool) [3] is an algorithm and program for comparing primary biological sequence information, such as the amino-acid sequences of proteins or the nucleotides of DNA and/or RNA sequences. A BLAST search enables a researcher to compare a subject protein or nucleotide sequence (called a query ...
Alignments for membrane protein sequences: Protein: Both: M. Stamm, K. Khafizov, R. Staritzbichler, L.R. Forrest: 2013 ALLALIGN For DNA, RNA and protein molecules up to 32MB, aligns all sequences of size K or greater. Similar alignments are grouped together for analysis. Automatic repetitive sequence filter. Both Local E. Wachtel 2017
Artistic 2.0 Fred Hutchinson Cancer Research Center: BioJava: Java library functions for manipulating sequences, protein structures, file parsers, CORBA interoperability, Distributed Annotation System (DAS), access to AceDB, dynamic programming, and simple statistical routines Linux, macOS, Windows: LGPL v2.1 Open Bioinformatics Foundation: BioJS
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 ...
BLAST, on the other hand, builds an index of the query sequences and searches through the database for matches. [1] A BLAST variant called MegaBLAST indexes 4 databases to speed up alignments. [9] BLAT can extend on multiple perfect and near-perfect matches (default is 2 perfect matches of length 11 for nucleotide searches and 3 perfect matches ...
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.
Modern sensitive methods for protein search utilize sequence profiles. They may be used to compare a sequence to a profile, or in more advanced cases such as HH-suite, to match among profiles. [2] [6] [7] [8] Profiles and alignments are themselves derived from matches, using for example PSI-BLAST or HHblits.
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.