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GRAph ALigner (GRAAL)
Graph Aligner (GRAAL)Oleksii Kuchaiev, Tijana Milenković, Vesna Memisević, Wayne Hayes, and Nataša Pržulj, Topological network alignment uncovers biological function and phylogeny, Journal of the Royal Society Interface 2010. is an algorithm for global network alignment that is based solely on network topology. It aligns two networks G and H by producing an alignment that consists of a set of ordered pairs (x, y), where x is a node in G and y is a node in H. GRAAL matches pairs of nodes originating in different networks based on their graphlet degree signature similarities,Tijana Milenkovic and Nataša Pržulj, Uncovering Biological Network Function via Graphlet Degree Signatures, Cancer Informatics 2008, 6:257–273. where a higher similarity between two nodes corresponds to a higher topological similarity between their extended neighborhoods (out to distance 4). GRAAL produces global alignments, i.e., it aligns each node in the smaller network to exactly one node in the larg ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Graphlets
Graphlets in mathematics are induced subgraph isomorphism classes in a graph,Pržulj N, Corneil DG, Jurisica I: Modeling Interactome, Scale-Free or Geometric?, Bioinformatics 2004, 20(18):3508-3515.Pržulj N, Biological Network Comparison Using Graphlet Degree Distribution, Bioinformatics 2007, 23:e177-e183. i.e. two graphlet occurrences are isomorphic, whereas two graphlets are non-isomorphic. Graphlets differ from network motifs in a statistical sense, network motifs are defined as over- or under-represented graphlets with respect to some random graph null model. Graphlet-based network properties Relative graphlet frequency distance RGF-distance compares the frequencies of the appearance of all 3-5-node graphlets in two networks. Let ''Ni(G)'' be the number of graphlets of type i (i \in \) in network ''G'', and let T(G) = \sum_^ N_i(G) be the total number of graphlets of ''G''. The "similarity" between two graphs should be independent of the total number of nodes or edges ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
BLAST (biotechnology)
In bioinformatics, BLAST (basic local alignment search tool) 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) with a library or database of sequences, and identify database sequences that resemble alphabet above a certain threshold. For example, following the discovery of a previously unknown gene in the mouse, a scientist will typically perform a BLAST search of the human genome to see if humans carry a similar gene; BLAST will identify sequences in the pig genome that resemble the mouse gene based on similarity of sequence. Background BLAST, which ''The New York Times'' called ''the Google of biological research'', is one of the most widely used bioinformatics programs for sequence searching. It addresses a fundamental problem in bioinformatics r ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Sequence Alignment
In bioinformatics, a sequence alignment is a way of arranging the sequences of DNA, RNA, or protein to identify regions of similarity that may be a consequence of functional, structural, or evolutionary relationships between the sequences. Aligned sequences of nucleotide or amino acid residues are typically represented as rows within a matrix. Gaps are inserted between the residues so that identical or similar characters are aligned in successive columns. Sequence alignments are also used for non-biological sequences, such as calculating the distance cost between strings in a natural language or in financial data. Interpretation If two sequences in an alignment share a common ancestor, mismatches can be interpreted as point mutations and gaps as indels (that is, insertion or deletion mutations) introduced in one or both lineages in the time since they diverged from one another. In sequence alignments of proteins, the degree of similarity between amino acids occupying a parti ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Footnotes
A note is a string of text placed at the bottom of a page in a book or document or at the end of a chapter, volume, or the whole text. The note can provide an author's comments on the main text or citations of a reference work in support of the text. Footnotes are notes at the foot of the page while endnotes are collected under a separate heading at the end of a chapter, volume, or entire work. Unlike footnotes, endnotes have the advantage of not affecting the layout of the main text, but may cause inconvenience to readers who have to move back and forth between the main text and the endnotes. In some editions of the Bible, notes are placed in a narrow column in the middle of each page between two columns of biblical text. Numbering and symbols In English, a footnote or endnote is normally flagged by a superscripted number immediately following that portion of the text the note references, each such footnote being numbered sequentially. Occasionally, a number between brack ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
