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Information Theory and Statistics

by S. Kullback , 1968
"... Entropy and relative entropy are proposed as features extracted from symbol sequences. Firstly, a proper Iterated Function System is driven by the sequence, producing a fractaMike representation (CSR) with a low computational cost. Then, two entropic measures are applied to the CSR histogram of th ..."
Abstract - Cited by 1805 (2 self) - Add to MetaCart
Entropy and relative entropy are proposed as features extracted from symbol sequences. Firstly, a proper Iterated Function System is driven by the sequence, producing a fractaMike representation (CSR) with a low computational cost. Then, two entropic measures are applied to the CSR histogram

Sequence Logos: A New Way to Display Consensus Sequences

by homas D. Schneider, Thomas D. Schneider, R. Michael Stephens - Nucleic Acids Res , 1990
"... INTRODUCTION A logo is "a single piece of type bearing two or more usually separate elements" [1]. In this paper, we use logos to display aligned sets of sequences. Sequence logos concentrate the following information into a single graphic [2]: 1. The general consensus of the sequences. ..."
Abstract - Cited by 650 (28 self) - Add to MetaCart
INTRODUCTION A logo is "a single piece of type bearing two or more usually separate elements" [1]. In this paper, we use logos to display aligned sets of sequences. Sequence logos concentrate the following information into a single graphic [2]: 1. The general consensus of the sequences

Base-calling of automated sequencer traces using phred. I. Accuracy Assessment

by Brent Ewing, Ladeana Hillier, Michael C. Wendl, Phil Green - GENOME RES , 1998
"... The availability of massive amounts of DNA sequence information has begun to revolutionize the practice of biology. As a result, current large-scale sequencing output, while impressive, is not adequate to keep pace with growing demand and, in particular, is far short of what will be required to obta ..."
Abstract - Cited by 1653 (4 self) - Add to MetaCart
The availability of massive amounts of DNA sequence information has begun to revolutionize the practice of biology. As a result, current large-scale sequencing output, while impressive, is not adequate to keep pace with growing demand and, in particular, is far short of what will be required

A greedy algorithm for aligning DNA sequences

by Zheng Zhang, Scott Schwartz, Lukas Wagner, Webb Miller - J. COMPUT. BIOL , 2000
"... For aligning DNA sequences that differ only by sequencing errors, or by equivalent errors from other sources, a greedy algorithm can be much faster than traditional dynamic programming approaches and yet produce an alignment that is guaranteed to be theoretically optimal. We introduce a new greedy a ..."
Abstract - Cited by 585 (16 self) - Add to MetaCart
For aligning DNA sequences that differ only by sequencing errors, or by equivalent errors from other sources, a greedy algorithm can be much faster than traditional dynamic programming approaches and yet produce an alignment that is guaranteed to be theoretically optimal. We introduce a new greedy

Some informational aspects of visual perception

by Fred Attneave - Psychol. Rev , 1954
"... The ideas of information theory are at present stimulating many different areas of psychological inquiry. In providing techniques for quantifying situations which have hitherto been difficult or impossible to quantify, they suggest new and more precise ways of conceptualizing these situations (see M ..."
Abstract - Cited by 643 (2 self) - Add to MetaCart
Miller [12] for a general discussion and bibliography). Events ordered in time are particularly amenable to informational analysis; thus language sequences are being extensively studied, and other sequences, such as those of music, plainly invite research. In this paper I shall indicate some of the ways

Controlled and automatic human information processing

by Walter Schneider, Richard M. Shiffrin - I. Detection, search, and attention. Psychological Review , 1977
"... A two-process theory of human information processing is proposed and applied to detection, search, and attention phenomena. Automatic processing is activa-tion of a learned sequence of elements in long-term memory that is initiated by appropriate inputs and then proceeds automatically—without subjec ..."
Abstract - Cited by 874 (16 self) - Add to MetaCart
A two-process theory of human information processing is proposed and applied to detection, search, and attention phenomena. Automatic processing is activa-tion of a learned sequence of elements in long-term memory that is initiated by appropriate inputs and then proceeds automatically

Incorporating non-local information into information extraction systems by Gibbs sampling

by Jenny Rose Finkel, Trond Grenager, Christopher Manning - IN ACL , 2005
"... Most current statistical natural language processing models use only local features so as to permit dynamic programming in inference, but this makes them unable to fully account for the long distance structure that is prevalent in language use. We show how to solve this dilemma with Gibbs sampling, ..."
Abstract - Cited by 730 (25 self) - Add to MetaCart
, a simple Monte Carlo method used to perform approximate inference in factored probabilistic models. By using simulated annealing in place of Viterbi decoding in sequence models such as HMMs, CMMs, and CRFs, it is possible to incorporate non-local structure while preserving tractable inference. We

Maximum entropy markov models for information extraction and segmentation

by Andrew McCallum, Dayne Freitag, Fernando Pereira , 2000
"... Hidden Markov models (HMMs) are a powerful probabilistic tool for modeling sequential data, and have been applied with success to many text-related tasks, such as part-of-speech tagging, text segmentation and information extraction. In these cases, the observations are usually modeled as multinomial ..."
Abstract - Cited by 561 (18 self) - Add to MetaCart
Hidden Markov models (HMMs) are a powerful probabilistic tool for modeling sequential data, and have been applied with success to many text-related tasks, such as part-of-speech tagging, text segmentation and information extraction. In these cases, the observations are usually modeled

Database resources of the National Center for Biotechnology Information

by David L. Wheeler, Tanya Barrett, Dennis A. Benson, Stephen H. Bryant, Kathi Canese, Vyacheslav Chetvernin, Deanna M. Church, Michael Dicuccio, Ron Edgar, Scott Federhen, Lewis Y. Geer, Yuri Kapustin, Oleg Khovayko, David L, David J. Lipman, Thomas L. Madden, Donna R. Maglott, James Ostell, Vadim Miller, Kim D. Pruitt, Gregory D. Schuler, Edwin Sequeira, Steven T. Sherry, Karl Sirotkin, Re Souvorov, Grigory Starchenko, Roman L. Tatusov, Tatiana A. Tatusova, Lukas Wagner, Eugene Yaschenko - Nucleic Acids Res , 2008
"... In addition to maintaining the GenBankÒ nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other biological data made available through NCBI’s Web site. NCBI resources include Entrez, ..."
Abstract - Cited by 979 (15 self) - Add to MetaCart
In addition to maintaining the GenBankÒ nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other biological data made available through NCBI’s Web site. NCBI resources include Entrez,

MAFFT version 5: improvement in accuracy of multiple sequence alignment

by Kazutaka Katoh, Kei-ichi Kuma, Hiroyuki Toh, Takashi Miyata - NUCLEIC ACIDS RES , 2005
"... The accuracy of multiple sequence alignment pro-gram MAFFT has been improved. The new version (5.3) of MAFFT offers new iterative refinement options, H-INS-i, F-INS-i and G-INS-i, in which pairwise alignment information are incorporated into objective function. These new options of MAFFT showed high ..."
Abstract - Cited by 801 (5 self) - Add to MetaCart
The accuracy of multiple sequence alignment pro-gram MAFFT has been improved. The new version (5.3) of MAFFT offers new iterative refinement options, H-INS-i, F-INS-i and G-INS-i, in which pairwise alignment information are incorporated into objective function. These new options of MAFFT showed
Results 1 - 10 of 29,199