Holbert, Daniel: Detecting motifs with EMOTIF-MAKER and MASIA: A critical comparison of two tools for finding protein motifs
... amino acid conservation for a particular position. EMOTIF-MAKER and MASIA take very different approaches to this problem: EMOTIF-MAKER uses predefined substitution groups, whereas MASIA measures conservation more quantitatively by using statistical methods in multidimensional property-space. Both ap ...
... amino acid conservation for a particular position. EMOTIF-MAKER and MASIA take very different approaches to this problem: EMOTIF-MAKER uses predefined substitution groups, whereas MASIA measures conservation more quantitatively by using statistical methods in multidimensional property-space. Both ap ...
Slides - UF CISE
... Build the tree incrementally, check pointing the tree after each portion has been attempted. 2 distinct traversal patterns exist both of which are used during construction. Very long construction time. These effects combine to limit the size of the tree that can be constructed and stored on ...
... Build the tree incrementally, check pointing the tree after each portion has been attempted. 2 distinct traversal patterns exist both of which are used during construction. Very long construction time. These effects combine to limit the size of the tree that can be constructed and stored on ...
Clustering
... varying conditions/time points. • Expression level is estimated by measuring the amount of mRNA for that particular gene. • A gene is active if it is being transcribed. • More mRNA usually indicates more gene activity. ...
... varying conditions/time points. • Expression level is estimated by measuring the amount of mRNA for that particular gene. • A gene is active if it is being transcribed. • More mRNA usually indicates more gene activity. ...
Knox, Kirstin : An Introduction To Motif Based Functional Classification of Large Protein Families
... multidomain families (instead of building up from pairwise sequence alignments) is to base the measure of similarity on the presence or absence of motifs that are likely to have functional relevance. While there are extensive databases of known patterns and profiles that have been built from alignme ...
... multidomain families (instead of building up from pairwise sequence alignments) is to base the measure of similarity on the presence or absence of motifs that are likely to have functional relevance. While there are extensive databases of known patterns and profiles that have been built from alignme ...
Pattern Recognition
... and verification problem or a multiple alignment problem. •Either of these class of problems is NP-Hard so most of the solutions that have been proposed use heuristics or ad hoc constraints to discover patterns effectively ...
... and verification problem or a multiple alignment problem. •Either of these class of problems is NP-Hard so most of the solutions that have been proposed use heuristics or ad hoc constraints to discover patterns effectively ...
Statistically Significant Patterns in DNA Sequences
... Expected frequency of motifs AGGTCA and ATATAT with length k = 3: Ek = fx k (N − k + 1) The expected number of a specific motif of length k is the probability of the motif (i.e. fx k ) multiplied with the number of substrings of length k (i.e. (N − k + 1)). Each word of length k has the same expecta ...
... Expected frequency of motifs AGGTCA and ATATAT with length k = 3: Ek = fx k (N − k + 1) The expected number of a specific motif of length k is the probability of the motif (i.e. fx k ) multiplied with the number of substrings of length k (i.e. (N − k + 1)). Each word of length k has the same expecta ...
WS Procs 975 x 65
... of (…)(AGG)(..) and (…)AGGTG. Since it takes O(l) time to convert a length-l substring to a motif and there are X length-l substrings in T, brute force method takes O(Xl3) time to get the list of O(Xl2) possible forms of motif. However, when a motif of a substring is considered, we can easily get an ...
... of (…)(AGG)(..) and (…)AGGTG. Since it takes O(l) time to convert a length-l substring to a motif and there are X length-l substrings in T, brute force method takes O(Xl3) time to get the list of O(Xl2) possible forms of motif. However, when a motif of a substring is considered, we can easily get an ...
Evaluation of existing motif detection tools on their
... 1. start with a random positioning of blocks (based on prior information on the expected number of motif sites/TFs and max number of motif sites per sequence) 2. update the motif model based on the current blocks (<-> PG) 3. scoring: leave out the blocks for one sequence (<-> PG) and calculate for e ...
... 1. start with a random positioning of blocks (based on prior information on the expected number of motif sites/TFs and max number of motif sites per sequence) 2. update the motif model based on the current blocks (<-> PG) 3. scoring: leave out the blocks for one sequence (<-> PG) and calculate for e ...
Motif Finding
... finding consensus is easy even with mutations in the sequences because we can simply construct the profile to find the motif (consensus) • But… the starting positions s are usually not given. How can we find the “best” profile ...
... finding consensus is easy even with mutations in the sequences because we can simply construct the profile to find the motif (consensus) • But… the starting positions s are usually not given. How can we find the “best” profile ...
Parallel Geometric Hashing Algorithm for Protein Tertiary Structure
... Algorithm is a popular and reliable method for protein function determination, protein searching, structure classification and structure alignment [2]. In this paper, we ...
... Algorithm is a popular and reliable method for protein function determination, protein searching, structure classification and structure alignment [2]. In this paper, we ...
Research Paper Commerce Mathematics Graph Theory: Importance
... represent migration path or movement between the regions. This information is important when looking at breeding patterns or tracking the spread of disease, and to study the impact of migration that affect other species. The Graphs are also widely used in medical ultrasound projections. Medical ultr ...
... represent migration path or movement between the regions. This information is important when looking at breeding patterns or tracking the spread of disease, and to study the impact of migration that affect other species. The Graphs are also widely used in medical ultrasound projections. Medical ultr ...
poster - Computer Science and Engineering
... applications in understanding diseases and, ultimately, in design of therapies. Several computational methods for predicting kinase-specific phosphorylation sites have been proposed, including motif-based methods that rely on PSSMs and HMMs. However, it is unclear how the different motif-based appro ...
... applications in understanding diseases and, ultimately, in design of therapies. Several computational methods for predicting kinase-specific phosphorylation sites have been proposed, including motif-based methods that rely on PSSMs and HMMs. However, it is unclear how the different motif-based appro ...
model - (DIMACS) Rutgers
... in the leaves and where internal nodes are labeled with inferred character state such that the total number of character insertions and deletion along edges is minimized. • Dollo parsimony – only one insertion per character is allowed ...
... in the leaves and where internal nodes are labeled with inferred character state such that the total number of character insertions and deletion along edges is minimized. • Dollo parsimony – only one insertion per character is allowed ...
Milestone10
... http://cs.wellesley.edu/~cs303/assignments/M10/modA.txt Where does this file come from? We took a gene (modA) in the bacterial organism Escherichia coli and BLASTed its sequence against the genomes of similar bacterial organisms. From the BLAST results, we selected 8 significant alignments from 8 di ...
... http://cs.wellesley.edu/~cs303/assignments/M10/modA.txt Where does this file come from? We took a gene (modA) in the bacterial organism Escherichia coli and BLASTed its sequence against the genomes of similar bacterial organisms. From the BLAST results, we selected 8 significant alignments from 8 di ...
Motif recognition - www.bioinf.org.uk
... distribution in the positive set (random model). •Z-score: one needs to estimate an average score and a standard deviation as a function of sequence length. Then, one uses the number of standard deviations each sequence is away from the average as the score. •e-value (Expect value): given a database ...
... distribution in the positive set (random model). •Z-score: one needs to estimate an average score and a standard deviation as a function of sequence length. Then, one uses the number of standard deviations each sequence is away from the average as the score. •e-value (Expect value): given a database ...
LecturesPartC
... Some families are characterized by two or more “sub”-motifs with variable spacing between them Deciding upon motif boundaries difficult Possible information in intervening sequences lost if only motifs are used ...
... Some families are characterized by two or more “sub”-motifs with variable spacing between them Deciding upon motif boundaries difficult Possible information in intervening sequences lost if only motifs are used ...
Nonconvex Optimization Is Combinatorial Optimization
... objective function, decomposes it into independent sub-functions consisting of independent sets of terms and variables, and then recurses on these sub-functions, summing the results of these recursive calls to get the evaluation of the function. Pseudocode of our algorithm is shown in Algorithm 1. T ...
... objective function, decomposes it into independent sub-functions consisting of independent sets of terms and variables, and then recurses on these sub-functions, summing the results of these recursive calls to get the evaluation of the function. Pseudocode of our algorithm is shown in Algorithm 1. T ...
Subnetwork hierarchies of biochemical pathways
... (for subnetwork detection) of the method of Schuster et al. makes it an important contribution to biochemical pathway analysis. A potential drawback of this method is that networks might have inherent non-local features not possible to be detected by local quantities such as degree. (Non-local effec ...
... (for subnetwork detection) of the method of Schuster et al. makes it an important contribution to biochemical pathway analysis. A potential drawback of this method is that networks might have inherent non-local features not possible to be detected by local quantities such as degree. (Non-local effec ...
tutorial5_12
... GOMO • GOMO takes DNA binding motifs to find putative target genes and analyze their associated GO terms. A list of significant GO terms that can be linked to the given motifs will be produced. • GOMO returns a list of GO-terms that are significantly associated with target genes of the motif. ...
... GOMO • GOMO takes DNA binding motifs to find putative target genes and analyze their associated GO terms. A list of significant GO terms that can be linked to the given motifs will be produced. • GOMO returns a list of GO-terms that are significantly associated with target genes of the motif. ...
Network chemistry, network toxicology, network informatics, and
... http://www.iaees.org/publications/journals/nb/nb.asp), and network pharmacology (Hopkins, 2007, 2008), network science has been successfully used in some areas of sciences. Using network theory and methodology to improve traditional sciences is proved to be an effective approach. In present study, I ...
... http://www.iaees.org/publications/journals/nb/nb.asp), and network pharmacology (Hopkins, 2007, 2008), network science has been successfully used in some areas of sciences. Using network theory and methodology to improve traditional sciences is proved to be an effective approach. In present study, I ...
Structure of biological networks
... of subgraphs that are overrepresented in comparison with other complex networks. Here, we are going to look at the common global topological properties of molecular interaction networks, as well as at local architectural features in terms of characteristic network motifs. ...
... of subgraphs that are overrepresented in comparison with other complex networks. Here, we are going to look at the common global topological properties of molecular interaction networks, as well as at local architectural features in terms of characteristic network motifs. ...
Networks Dynamics
... signaling protein in this cellular context and then biochemically validate this finding by shRNA-mediated silencing of this kinase, followed by gene expression profile analysis. Gene expression data have been also utilized in the work of Tamada et al. which combines protein-protein interaction netwo ...
... signaling protein in this cellular context and then biochemically validate this finding by shRNA-mediated silencing of this kinase, followed by gene expression profile analysis. Gene expression data have been also utilized in the work of Tamada et al. which combines protein-protein interaction netwo ...
Integer Program Approach to Protein Threading
... A protein is composed of a central backbone and a collection of (typically) 50-2000 amino acids (a.k.a. residues). There are 20 different kinds of amino acids each consisting of up to 18 atoms, e.g., ...
... A protein is composed of a central backbone and a collection of (typically) 50-2000 amino acids (a.k.a. residues). There are 20 different kinds of amino acids each consisting of up to 18 atoms, e.g., ...
Bioinformatics 3 V 5 – Robustness and Modularity
... strongly supports suggested modular architecture of biological networks. There exist 2 types of clusters: protein complexes and dynamic functional modules. Both have more interactions among their members than with the rest of the network. Dynamic modules cannot be purified in experiments because the ...
... strongly supports suggested modular architecture of biological networks. There exist 2 types of clusters: protein complexes and dynamic functional modules. Both have more interactions among their members than with the rest of the network. Dynamic modules cannot be purified in experiments because the ...
Network motif
All networks, including biological networks, social networks, technological networks (e.g., computer networks and electrical circuits) and more, can be represented as graphs, which include a wide variety of subgraphs. One important local property of networks are so-called network motifs, which are defined as recurrent and statistically significant sub-graphs or patterns.Network motifs are sub-graphs that repeat themselves in a specific network or even among various networks. Each of these sub-graphs, defined by a particular pattern of interactions between vertices, may reflect a framework in which particular functions are achieved efficiently. Indeed, motifs are of notable importance largely because they may reflect functional properties. They have recently gathered much attention as a useful concept to uncover structural design principles of complex networks. Although network motifs may provide a deep insight into the network’s functional abilities, their detection is computationally challenging.