mining new motifs from cdna sequence data

... Definition (Sequence and sequence database) A sequence over an alphabet Σ is a finite sequence of symbols belonging to Σ, e.g., protein sequence is sequence over a 20-letter alphabet For any sequence ... functional regions of a novel sequence directly by mining its sequence along with a set of homologues found in sequence database (MAGIIC-PRO, [8]) Similar to multiple sequence alignment (MSA), MAGIIC-PRO ... defined as the number of symbols in S An input sequence database D contains a set of sequences In general, the input sequence database is a set of protein sequences that are presumed to be functionally...

Ngày tải lên: 12/08/2014, 17:20

Ngày tải lên: 20/06/2014, 01:20

... far is it from Boston to Seattle” ,“distance from Boston to Seattle”) S1 = {Boston}:(“how far is it from X1 to Seattle” ,“distance from X1 to Seattle”) S2 = {Seattle}:(“how far is it from Boston ... ,“distance from Boston to X1 ”) S3 = {Boston, Seattle}:(“how far is it from X1 to X2 ” ,“distance from X1 to X2 ”) P= { (p,pr)} Generating Reformulation Patterns Pattern Base O nline Phase New Question ... corresponding reformulation patterns q new : how good is the eden pure air system q new : how to market a restaurant ⋆ p : how good is the X p⋆ : how to market a X new new qr pr qr pr eden pure air system...

Ngày tải lên: 07/03/2014, 18:20

... polycephalum) With respect to the corresponding sequence to the Drosophila TGase, cDNA sequence was searched from database with the TBLASTN search engine to identify cDNA with homology to vertebrate TGases ... bp was produced by two successive reactions In the amino acid sequence deduced from the amplified cDNA sequence, a 15-amino acid sequence, which was determined by protein sequencing, was observed ... region Finally, a full-size composite cDNA sequence encoding PpTGase was obtained from the nucleotide sequences of the three RACE products The full-length cDNA of PpTGase was 2624 bp long and...

Ngày tải lên: 17/03/2014, 23:20

... repeat sequences The genome-wide coverage of sequencing data provides information about repetitive sequences beyond that captured by the canonical sequences, and our method, which incorporates sequence ... each repeat type as defined in the Repbase database The sequence of each entry is composed of the canonical repeat sequence concatenated with all instance sequences identified by the default RepeatMasker ... were excluded from the analysis The mm9 assembly was used for mouse data, the hg18 assembly for human data In all analyses, only alignments with at most one mismatch were admitted Dataset size...

Ngày tải lên: 09/08/2014, 20:22

... seed sequence, and mer3-8 utilizes nucleotides to of the sequence (b) Motif matches for the two Quaking motifs in 3’ UTRs, 5’ UTRs, coding regions and introns (c) Motif matches for the Pumilio dataset ... of sequence- specific RBPs (PUM2, QKI and IGF2BP1) revealed the strengths and current limitations of the PAR-CLIP protocol, and as a consequence, methods for the analysis of PAR-CLIP data PUM2 data ... of four distinct mRNA-interacting factors Three of the datasets were generated from immunoprecipitation data of the sequence- specific RBPs Quaking (QKI), Pumilio2 (PUM2), and Insulin-like growth...

Ngày tải lên: 09/08/2014, 23:20

... DataSet ds = new DataSet( ); // Fill the Orders table and add it to the DataSet SqlDataAdapter da = new SqlDataAdapter("SELECT * FROM Orders", ConfigurationSettings.AppSettings["Sql_ConnectString"]); ... ConfigurationSettings.AppSettings["Sql_ConnectString"]); DataTable ordersTable = new DataTable(ORDERS_TABLE); da.Fill(ordersTable); ds.Tables.Add(ordersTable); // Fill the OrderDetails table and add it to the DataSet da = new SqlDataAdapter("SELECT ... DataSet da = new SqlDataAdapter("SELECT * FROM [Order Details]", ConfigurationSettings.AppSettings["Sql_ConnectString"]); DataTable orderDetailsTable = new DataTable(ORDERDETAILS_TABLE); da.Fill(orderDetailsTable);...

Ngày tải lên: 21/01/2014, 11:20

... private void UpdateDataFromDifferentDataSourceForm_Load(object sender, System.EventArgs e) { // Create the DataAdapter for the source records daSource = new SqlDataAdapter("SELECT * FROM Customers", ... table to the grid dataGridSource.DataSource = dsSource.Tables["Customers"].DefaultView; // Create the DataAdapter for the destination records daDest = new SqlDataAdapter("SELECT * FROM Customers", ... tracks changes made to data by maintaining multiple versions of each row allowing the data to be reconciled later to a data source using a DataAdapter The data source to which the DataSet is reconciled...

Ngày tải lên: 21/01/2014, 11:20

... of the data sets helped considerably with the GLS estimation process, THE ESTIMATION OF R(t) FROM DISEASE OUTBREAK DATA Figure Model fits obtained using GLS on truncated influenza data from season ... al.), Springer, New York, to appear THE ESTIMATION OF R(t) FROM DISEASE OUTBREAK DATA 281 Figure Residuals plots from OLS estimation applied to the SEIR-generated synthetic data set (a) Residuals ... higher with the truncated data set than for the full data set, as should be expected given the reduced number of data points Overall, the results using OLS with the truncated data were less than satisfactory...

Ngày tải lên: 13/02/2014, 16:20

... B Liu 2004a Mining and Summarizing Customer Reviews In Proceedings of the 2004 ACM SIGKDD international conference on Knowledge discovery and data mining, pages 168-177 ACM Press New York, NY, ... we run our algorithm on the data and evaluate the precision and recall We also run the algorithms described in Hu and Liu (2004a) on the same data as the baseline From Table 2, we can see the ... S Corston-Oliver, and E Ringger 2005 Pulse: Mining Customer Opinions from Free Text In Proceedings of the 6th International Symposium on Intelligent Data Analysis After the summary is given, for...

Ngày tải lên: 20/02/2014, 09:20

... acid residue was calculated from a database of 3769 three-dimensional protein structures (which have < 25% sequence identity between each other) obtained from the SCOP database [37], containing ... regions from protein sequence Bioinformatics 26, 326–332 Murzin AG, Brenner SE, Hubbard T & Chothia C (1995) SCOP: a structural classification of proteins database for the investigation of sequences ... against a database of 57 amyloidogenic proteins in which the location of aggregation hot-spots was known from experiment) This average is called a4v [22] A plot of a4v over the entire sequence...

Ngày tải lên: 06/03/2014, 00:20

... THE HISTORY OF AUSTRALIA AND NEW ZEALAND FROM 1606 TO 1890 BY ALEXANDER SUTHERLAND, M.A AND GEORGE SUTHERLAND, M.A LONDON LONGMANS, GREEN, AND CO AND NEW YORK: 15 EAST 16th STREET GEORGE ... Melbourne, 183 A Maori Dwelling, 185 Milford Sound, South Island, New Zealand, 191 Rev S Marsden, “the Apostle of New Zealand,” 195 Auckland, from the Wharf, 206 Stronghold of the Maoris at Rangiriri, ... 1890, 163 XXI New South Wales, 1860 to 1890, 168 XXII Victoria, 1855 to 1890, 175 XXIII The Times of the Maoris, 184 XXIV New Zealand Colonised, 200 XXV White Men and Maoris, 215 XXVI New Zealand,...

Ngày tải lên: 06/03/2014, 12:21

... in the database (NCBI blast; http://www.ncbi.nlm.nih.gov) include adenylyl-sulfate kinase from Anaeromyxobacter sp Fw109-5 (GI:121539501), the predicted glutamatedependent NAD(+) synthase from ... ETFs An alignment of a- and b-ETFs from all kingdoms of life (Fig 2) shows that, within the a-ETF family, the overall sequence homology is low, although high sequence homology is found in the ... located approximately 4–6 A from the 8-a-methyl group of FMN [36] The physiological terminal electron acceptor of TMADH from M methylotrophus is ETF, with electron transfer from the [4Fe)4S]2+ ⁄ +...

Ngày tải lên: 07/03/2014, 05:20

... Figure using the training data from Section 4.2 over 100 EM iterations, with two folds per model For Model IM, we varied the number of user intents (K) in intervals from 100 to 400 (see Figure ... Domainindependent entity extraction from web search query logs In Proceedings of WWW ’11, pages 63–64, New York, NY, USA ACM Bernard J Jansen, Danielle L Booth, and Amanda Spink 2007 Determining the user intent ... sufficient amount of training data to estimate all parameters reliably In addition, our approach enabled us to learn (and perform inference in) the model with large amounts of data with reasonable computing...

Ngày tải lên: 07/03/2014, 18:20

... the state-of-the-art results with both dependency parsing data derived from PTB-III (Koo et al., 2008), and the CoNLL’03 shared task data (Turian et al., 2010) By comparing COFER with iCWR we ... Chen et al., 2009; Suzuki et al., 2009) For the supervised datasets, we used CoNLL’03 (Tjong Kim Sang and De Meulder, 2003) shared task data for NER, and the Penn Treebank III 639 (PTB) corpus ... (Marcus et al., 1994) for dependency parsing We prepared a total of 3.72 billion token text data as unsupervised data following the instructions given in (Suzuki et al., 2009) 4.1 Comparative Methods...

Ngày tải lên: 07/03/2014, 22:20

... multiple local newspapers in English and Chinese Our challenge is to find the translation of ~ / l i o u g a n and other words from this online nonparallel, comparable corpus of newspaper materials ... corpus of newspaper materials We choose to use issues of the English newspaper Hong Kong Standard and the Chinese newspaper Mingpao, from Dec.12,97 to Dec.31,97, as our corpus The English text contains ... Ricardo Baeza-Yates, editors 1992 Information Retrieval: Data structures ~ Algorithms Prentice-Hall Pascale Fung and Kenneth Church 1994 Kvec: A new approach for aligning parallel texts In Proceedings...

Ngày tải lên: 08/03/2014, 05:21

... blow it up on the xerox machine and paste it up to start your scene This set of notes shows a sequence from Disney’s Rescuers where the animator has worked out his staging and action in a series...

Ngày tải lên: 08/03/2014, 11:20

... acid sequence was compared with known protein sequences in the nucleotide/protein sequence databases by the BLAST program from the Swiss-Prot database Sequence alignment was carried out using the ... were purchased from Sigma Chemical Co DEAE-Toyopearl 650 M and Butyl-Toyopearl 650 M were from Tosoh (Tokyo, Japan) FPLC-Mono Q was from Pharmacia Substrates and standards were from commercial ... DNA ligase were from New BioLabs and Gibco BRL Pfu DNA polymerase and alkaline phosphatase were from Promega and Boehringer Mannheim, respectively D-Amino acid oxidase (EC 1.4.3.3) from porcine...

Ngày tải lên: 08/03/2014, 16:20

Ngày tải lên: 16/03/2014, 03:20

... collections of data to be ordered The object-relational database systemIllustra [I11941 provides database support for time-seriesdata along with relational data A time-seriesis an ADT(Abstract Data Type) ... Domain who are primarily interested in sequencedata, for example, to directly query named sequences without having to embed Figure 1: Data Sequence the sequences inside relational tuples While ... in the sequence The DBMS should efficiently processqueriesover largedisk-based sequences Further, in most applications, there is sequence data as well as relational and other kinds of data Complex...

Ngày tải lên: 16/03/2014, 16:20