Aalborg Universitet Real-Time Implementations of Sparse Linear Prediction for Speech Processing
... There are many methods for solving the sparse LPC (5). In this paper, we will focus on primal-dual interior-point methods. The purpose is twofold. Firstly, these are well known efficient methods for convex optimization used in real-time convex optimization [19, 20]; Secondly, by comparing the propos ...
... There are many methods for solving the sparse LPC (5). In this paper, we will focus on primal-dual interior-point methods. The purpose is twofold. Firstly, these are well known efficient methods for convex optimization used in real-time convex optimization [19, 20]; Secondly, by comparing the propos ...
Speeding Up HMM Decoding and Training by Exploiting Sequence
... regions are typically a few hundred to a few thousand nucleotides long, located around the promoters of many genes. As such, they are useful landmarks for the identification of genes. The observed sequence (X) is a long DNA sequence composed of four possible nucleotides (Σ = {A, C, G, T }). The leng ...
... regions are typically a few hundred to a few thousand nucleotides long, located around the promoters of many genes. As such, they are useful landmarks for the identification of genes. The observed sequence (X) is a long DNA sequence composed of four possible nucleotides (Σ = {A, C, G, T }). The leng ...
Sequential Pattern Mining with Constraints on Large Protein
... cells, tissues and organisms, and are the most common target of prescription drugs [3]. Despite their biological importance, there are only a small number of IMPs whose 3D structure information is available. Predicting the secondary structure of IMPs using machine learning techniques is an active ar ...
... cells, tissues and organisms, and are the most common target of prescription drugs [3]. Despite their biological importance, there are only a small number of IMPs whose 3D structure information is available. Predicting the secondary structure of IMPs using machine learning techniques is an active ar ...
Looking for Darwin in Genomic Sequences—Validity and Success of
... Hughes (2007) criticized the site-based LRTs (Nielsen and Yang 1998; Yang et al. 2000) and the parsimony method of Suzuki and Gojobori (1999) for lacking prior biological hypotheses about which codons are potentially under positive selection, likening them to an undirected ‘‘fishing expedition’’ (Hu ...
... Hughes (2007) criticized the site-based LRTs (Nielsen and Yang 1998; Yang et al. 2000) and the parsimony method of Suzuki and Gojobori (1999) for lacking prior biological hypotheses about which codons are potentially under positive selection, likening them to an undirected ‘‘fishing expedition’’ (Hu ...
Scoring Matrices CS795
... Play the most critical role in determining how two sequences align with each other. ...
... Play the most critical role in determining how two sequences align with each other. ...
Archives of microbiology
... state, its optimal growth occurs at 10 % sucrose and pH 5.5 (Gillis et al. 1989; Stephan et al. 1991), and can fix nitrogen in the presence of 30 % sucrose at pH 3.0. However, its nitrogenase activity is partially inhibited by NH4+ at high sucrose concentrations, and it is not affected by the high c ...
... state, its optimal growth occurs at 10 % sucrose and pH 5.5 (Gillis et al. 1989; Stephan et al. 1991), and can fix nitrogen in the presence of 30 % sucrose at pH 3.0. However, its nitrogenase activity is partially inhibited by NH4+ at high sucrose concentrations, and it is not affected by the high c ...
Reverse transcription-pcr (rt-pcr)
... The idea of RT-PCR is based upon retroviruses. Retroviruses have an RNA rather than DNA genome. So they must use reverse transcriptase (RT) to covert their RNA genomes into DNA. Human Immunodeficiency Virus (HIV) is an example of a retrovirus. ...
... The idea of RT-PCR is based upon retroviruses. Retroviruses have an RNA rather than DNA genome. So they must use reverse transcriptase (RT) to covert their RNA genomes into DNA. Human Immunodeficiency Virus (HIV) is an example of a retrovirus. ...
Assay Standards Working Group Recommendations, November 2012
... for the definition of reference epigenomes to be included within the International Human Epigenome Consortium. These recommendations are minimal standards based on current knowledge of the elements contributing to epigenomic regulation in human cells and the current state of epigenomic mapping techn ...
... for the definition of reference epigenomes to be included within the International Human Epigenome Consortium. These recommendations are minimal standards based on current knowledge of the elements contributing to epigenomic regulation in human cells and the current state of epigenomic mapping techn ...
RNA-Seq - Tufts University
... The problem with the solution de Bruijn graphs are resolved into the simplest paths after all reads are taken into account Since these reads are stored in memory, more reads requires much larger amounts of RAM High RAM node on the cluster? ...
... The problem with the solution de Bruijn graphs are resolved into the simplest paths after all reads are taken into account Since these reads are stored in memory, more reads requires much larger amounts of RAM High RAM node on the cluster? ...
Global Sequence Alignment by Dynamic Programming
... to solve, simply solve all smaller problems, store the answers and assembled them later to a solution for the large problem. ...
... to solve, simply solve all smaller problems, store the answers and assembled them later to a solution for the large problem. ...
bluebird bio, Inc. - corporate
... Progress to late-stage clinical development of lentivirus based gene therapies and CAR T therapies will require enhanced characterization of the purified lentivirus product. LVV preparations are complex and utilize host cells that produce not only the viral particles of interest, but also a vari ...
... Progress to late-stage clinical development of lentivirus based gene therapies and CAR T therapies will require enhanced characterization of the purified lentivirus product. LVV preparations are complex and utilize host cells that produce not only the viral particles of interest, but also a vari ...
plasmid
... Other plasmid cloning vectors pBR322 was a well conceived cloning vector but has few cloning sites selection procedure is time consuming pUC19 is a plasmid cloning vector created by Messing and co-workers in the University of ...
... Other plasmid cloning vectors pBR322 was a well conceived cloning vector but has few cloning sites selection procedure is time consuming pUC19 is a plasmid cloning vector created by Messing and co-workers in the University of ...
Co-evolving residues in membrane proteins
... Pazos et al., 1997). It was also shown that networks of correlated mutations tend to appear near binding regions and active sites (Gloor et al., 2005) allowing for the identification of functionally important regions in combination with entropic measures (Saraf et al., 2003). Lately, WW domain seque ...
... Pazos et al., 1997). It was also shown that networks of correlated mutations tend to appear near binding regions and active sites (Gloor et al., 2005) allowing for the identification of functionally important regions in combination with entropic measures (Saraf et al., 2003). Lately, WW domain seque ...
q-gram Based Database Searching Using a Suffix Array (QUASAR)
... is due to the combination of the power of biomolecular sequence comparison with the ease-ofuse of tools for searching such databases for sequences exhibiting similarity to a given query sequence. These searches are nowadays routine and vital for molecular biology because they serve to \generate new ...
... is due to the combination of the power of biomolecular sequence comparison with the ease-ofuse of tools for searching such databases for sequences exhibiting similarity to a given query sequence. These searches are nowadays routine and vital for molecular biology because they serve to \generate new ...
a review of artificial intelligence based building energy prediction
... SVR provides a better balance between prediction accuracy and computation speed comparing with MLR and ANNs. High level of prediction accuracy can be achieved by SVR once parameters are appropriately selected. The limitation of SVR method is the determination of kernel function. There is no uniform ...
... SVR provides a better balance between prediction accuracy and computation speed comparing with MLR and ANNs. High level of prediction accuracy can be achieved by SVR once parameters are appropriately selected. The limitation of SVR method is the determination of kernel function. There is no uniform ...
Expression of gene encoding immunodominant merozoite surface
... The duplicate wells of ELISA plate were coated separately with Tams1 protein at a concentration of 1,2 or 5 µg per mL of carbonate-bicarbonate buffer (pH 9.6) and titrated with two positive and two negative bovine sera diluted 1:50, 1:100 or 1:200 with PBS (pH 7.2) in standard ELISA format10. The co ...
... The duplicate wells of ELISA plate were coated separately with Tams1 protein at a concentration of 1,2 or 5 µg per mL of carbonate-bicarbonate buffer (pH 9.6) and titrated with two positive and two negative bovine sera diluted 1:50, 1:100 or 1:200 with PBS (pH 7.2) in standard ELISA format10. The co ...
Chapter 20
... Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings ...
... Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings ...
Lecture 4: Lecture Notes + Textbook
... This procedure is performed by four reaction mixtures at the same time In all of these mixtures, DNA polymerase is used to make the complement of a particular sequence It is primed by a fragment that contains the complementary sequence to a known sequence What makes this method special is its use of ...
... This procedure is performed by four reaction mixtures at the same time In all of these mixtures, DNA polymerase is used to make the complement of a particular sequence It is primed by a fragment that contains the complementary sequence to a known sequence What makes this method special is its use of ...
In vitro selection of restriction endonucleases by
... FokI is a type IIS restriction endonuclease isolated from Flavobacterium okeanokoites and recognizes the nonpalindromic nucleotide sequence 50 -GGATG(N)9/13-30 (16). FokI comprises two separate domains: a DNA recognition domain that binds the recognition sequence specifically and a catalytic domain ...
... FokI is a type IIS restriction endonuclease isolated from Flavobacterium okeanokoites and recognizes the nonpalindromic nucleotide sequence 50 -GGATG(N)9/13-30 (16). FokI comprises two separate domains: a DNA recognition domain that binds the recognition sequence specifically and a catalytic domain ...
Selection Vector for Direct Cloning of Proof Reading Polymerase
... We have compared cloning efficiency of pUC18ccdB with the commercially available highly efficient PCR cloning kit pCR®2.1-TOPO. Whereas pUC18ccdB relies on positive selection through disruption of the ccdB suicide gene, pCR®2.1-TOPO relies on vaccinia virus derived topoisomerase I. This enzyme binds ...
... We have compared cloning efficiency of pUC18ccdB with the commercially available highly efficient PCR cloning kit pCR®2.1-TOPO. Whereas pUC18ccdB relies on positive selection through disruption of the ccdB suicide gene, pCR®2.1-TOPO relies on vaccinia virus derived topoisomerase I. This enzyme binds ...
10. Hidden Markov Models (HMM) for Speech Processing
... Given the observation sequence O = o1 o2 … oT, and a model λ, how do we choose a corresponding state sequence Q = q1 q2 … qT which is optimal in some meaningful sense (i.e., best “explains” the observations)? i.e. maximizes P(Q, O|λ) The forward algorithm provides the total probability through all p ...
... Given the observation sequence O = o1 o2 … oT, and a model λ, how do we choose a corresponding state sequence Q = q1 q2 … qT which is optimal in some meaningful sense (i.e., best “explains” the observations)? i.e. maximizes P(Q, O|λ) The forward algorithm provides the total probability through all p ...
CopyRight v2.0 BAC Cloning Kits
... CopyRight pSMART® BAC vectors: The CopyRight pSMART BAC cloning vector (Figure 1) incorporates transcription-free cloning for the highest stability BAC cloning. The vector is supplied precut at a choice of BamHI, EcoRI, or HindIII sites, with dephosphorylated ends. Insert DNAs with 5phosphorylated ...
... CopyRight pSMART® BAC vectors: The CopyRight pSMART BAC cloning vector (Figure 1) incorporates transcription-free cloning for the highest stability BAC cloning. The vector is supplied precut at a choice of BamHI, EcoRI, or HindIII sites, with dephosphorylated ends. Insert DNAs with 5phosphorylated ...
Coupled prediction of protein secondary and tertiary structure
... to use the network trained on native structures rather than retraining it with ROSETTA models. This choice allowed the use of as many native structures as possible for training, not only of proteins with ⬍180 aa as foldable with ROSETTA. A ‘‘moving target’’ effect is avoided in which improvements in ...
... to use the network trained on native structures rather than retraining it with ROSETTA models. This choice allowed the use of as many native structures as possible for training, not only of proteins with ⬍180 aa as foldable with ROSETTA. A ‘‘moving target’’ effect is avoided in which improvements in ...
Gene prediction
In computational biology gene prediction or gene finding refers to the process of identifying the regions of genomic DNA that encode genes. This includes protein-coding genes as well as RNA genes, but may also include prediction of other functional elements such as regulatory regions. Gene finding is one of the first and most important steps in understanding the genome of a species once it has been sequenced.In its earliest days, ""gene finding"" was based on painstaking experimentation on living cells and organisms. Statistical analysis of the rates of homologous recombination of several different genes could determine their order on a certain chromosome, and information from many such experiments could be combined to create a genetic map specifying the rough location of known genes relative to each other. Today, with comprehensive genome sequence and powerful computational resources at the disposal of the research community, gene finding has been redefined as a largely computational problem.Determining that a sequence is functional should be distinguished from determining the function of the gene or its product. Predicting the function of a gene and confirming that the gene prediction is accurate still demands in vivo experimentation through gene knockout and other assays, although frontiers of bioinformatics research are making it increasingly possible to predict the function of a gene based on its sequence alone.Gene prediction is one of the key steps in Genome annotation, following Sequence assembly, the filtering of non-coding regions and repeat masking.Gene prediction is closely related to the so called 'target search problem' investigating how DNA-binding proteins (transcription factors) locate specific binding sites within the genome. Many aspects of structural gene prediction are based on current understanding of underlying biochemical processes in the cell such as gene transcription, translation, protein–protein interactions and regulation processes, which are subject of active research in the various Omics fields such as Transcriptomics, Proteomics, Metabolomics, and more generally structural and functional genomics.