Results 1 - 10 of 26,185

COMPASS: a tool for comparison of multiple protein alignments with assessment of statistical significance

by Ruslan Sadreyev, Nick Grishin, Howard Hughes Medical - J. Mol. Biol , 2003
"... We present a novel method for the comparison of multiple protein align-ments with assessment of statistical significance (COMPASS). The method derives numerical profiles from alignments, constructs optimal local profile–profile alignments and analytically estimates E-values for the detected similari ..."
Abstract - Cited by 125 (33 self) - Add to MetaCart
We present a novel method for the comparison of multiple protein align-ments with assessment of statistical significance (COMPASS). The method derives numerical profiles from alignments, constructs optimal local profile–profile alignments and analytically estimates E-values for the detected

Multiple sequence alignment with the Clustal series of programs

by Ramu Chenna, Hideaki Sugawara, Tadashi Koike, Rodrigo Lopez, Toby J. Gibson, Desmond G. Higgins, Julie D. Thompson - Nucleic Acids Res , 2003
"... The Clustal series of programs are widely used in molecular biology for the multiple alignment of both nucleic acid and protein sequences and for preparing phylogenetic trees. The popularity of the programs depends on a number of factors, including not only the accuracy of the results, but also the ..."
Abstract - Cited by 747 (5 self) - Add to MetaCart
The Clustal series of programs are widely used in molecular biology for the multiple alignment of both nucleic acid and protein sequences and for preparing phylogenetic trees. The popularity of the programs depends on a number of factors, including not only the accuracy of the results, but also

Muscle: multiple sequence alignment with high accuracy and high throughput

by Robert C. Edgar - NUCLEIC ACIDS RES , 2004
"... We describe MUSCLE, a new computer program for creating multiple alignments of protein sequences. Elements of the algorithm include fast distance estimation using kmer counting, progressive alignment using a new profile function we call the logexpectation score, and refinement using tree-dependent r ..."
Abstract - Cited by 2509 (7 self) - Add to MetaCart
We describe MUSCLE, a new computer program for creating multiple alignments of protein sequences. Elements of the algorithm include fast distance estimation using kmer counting, progressive alignment using a new profile function we call the logexpectation score, and refinement using tree

DIALIGN-TX and multiple protein alignment using secondary structure information at GOBICS

by Amarendran R. Subramanian, Suvrat Hiran, Rasmus Steinkamp, Peter Meinicke, Eduardo Corel, Burkhard Morgenstern , 2010
"... ..."
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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

Pfam protein families database

by Robert D. Finn, John Tate, Jaina Mistry, Penny C. Coggill, Stephen John Sammut, Hans-rudolf Hotz, Goran Ceric, Kristoffer Forslund, Sean R. Eddy, Erik L. L. Sonnhammer, Alex Bateman - Nucleic Acids Research, 2008, 36(Database issue): D281–D288
"... Pfam is a comprehensive collection of protein domains and families, represented as multiple sequence alignments and as profile hidden Markov models. The current release of Pfam (22.0) contains 9318 protein families. Pfam is now based not only on the UniProtKB sequence database, but also on NCBI GenP ..."
Abstract - Cited by 771 (13 self) - Add to MetaCart
Pfam is a comprehensive collection of protein domains and families, represented as multiple sequence alignments and as profile hidden Markov models. The current release of Pfam (22.0) contains 9318 protein families. Pfam is now based not only on the UniProtKB sequence database, but also on NCBI Gen

Globally Consistent Range Scan Alignment for Environment Mapping

by F. Lu, E. Milios - AUTONOMOUS ROBOTS , 1997
"... A robot exploring an unknown environmentmay need to build a world model from sensor measurements. In order to integrate all the frames of sensor data, it is essential to align the data properly. An incremental approach has been typically used in the past, in which each local frame of data is alig ..."
Abstract - Cited by 531 (8 self) - Add to MetaCart
is aligned to a cumulative global model, and then merged to the model. Because different parts of the model are updated independently while there are errors in the registration, such an approachmay result in an inconsistent model. In this paper, we study the problem of consistent registration of multiple

Hidden Markov models in computational biology: applications to protein modeling

by Anders Krogh, Michael Brown, I. Saira Mian, Kimmen Sjölander, David Haussler - JOURNAL OF MOLECULAR BIOLOGY , 1994
"... Hidden.Markov Models (HMMs) are applied t.0 the problems of statistical modeling, database searching and multiple sequence alignment of protein families and protein domains. These methods are demonstrated the on globin family, the protein kinase catalytic domain, and the EF-hand calcium binding moti ..."
Abstract - Cited by 655 (39 self) - Add to MetaCart
Hidden.Markov Models (HMMs) are applied t.0 the problems of statistical modeling, database searching and multiple sequence alignment of protein families and protein domains. These methods are demonstrated the on globin family, the protein kinase catalytic domain, and the EF-hand calcium binding

Fitting a mixture model by expectation maximization to discover motifs in biopolymers.

by Timothy L Bailey , Charles Elkan - Proc Int Conf Intell Syst Mol Biol , 1994
"... Abstract The algorithm described in this paper discovers one or more motifs in a collection of DNA or protein sequences by using the technique of expect~tiou ma.,dmization to fit a two-component finite mixture model to the set of sequences. Multiple motifs are found by fitting a mixture model to th ..."
Abstract - Cited by 947 (5 self) - Add to MetaCart
Abstract The algorithm described in this paper discovers one or more motifs in a collection of DNA or protein sequences by using the technique of expect~tiou ma.,dmization to fit a two-component finite mixture model to the set of sequences. Multiple motifs are found by fitting a mixture model

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.

by Stephen F Altschul , Thomas L Madden , Alejandro A Schäffer , Jinghui Zhang , Zheng Zhang , Webb Miller , David J Lipman - Nucleic Acids Res. , 1997
"... ABSTRACT The BLAST programs are widely used tools for searching protein and DNA databases for sequence similarities. For protein comparisons, a variety of definitional, algorithmic and statistical refinements described here permits the execution time of the BLAST programs to be decreased substantia ..."
Abstract - Cited by 8572 (88 self) - Add to MetaCart
ABSTRACT The BLAST programs are widely used tools for searching protein and DNA databases for sequence similarities. For protein comparisons, a variety of definitional, algorithmic and statistical refinements described here permits the execution time of the BLAST programs to be decreased
Results 1 - 10 of 26,185