Results 1 - 10 of 295

E.: Automatic clustering of orthologs and inparalogs from pairwise species comparisons.

by Maido Remm , Christian E V Storm , Erik L L Sonnhammer - Journal of Molecular Biology , 2001
"... Orthologs are genes in different species that originate from a single gene in the last common ancestor of these species. Such genes have often retained identical biological roles in the present-day organisms. It is hence important to identify orthologs for transferring functional information betwee ..."
Abstract - Cited by 311 (9 self) - Add to MetaCart
with phylogenetic methods, but these are slow and dif®cult to automate. Automatic clustering methods based on two-way best genome-wide matches on the other hand, have so far not separated in-paralogs from out-paralogs effectively. We present a fully automatic method for ®nding orthologs and inparalogs from two

Extracting protein alignment models from the sequence database

by Andrew F. Neuwald, Jun S. Liu, David J. Lipman, Charles E. Lawrence - Nucleic Acids Research , 1997
"... Biologists often gain structural and functional insights into a protein sequence by constructing a multiple alignment model of the family. Here a program called PROBE fully automates this process of model construction starting from a single sequence. Central to this program is a powerful new method ..."
Abstract - Cited by 76 (7 self) - Add to MetaCart
Biologists often gain structural and functional insights into a protein sequence by constructing a multiple alignment model of the family. Here a program called PROBE fully automates this process of model construction starting from a single sequence. Central to this program is a powerful new method

DT: GenTHREADER: an efficient and reliable protein fold recognition method for genomic sequences

by David T. Jones - J Mol Biol , 1999
"... A new protein fold recognition method is described which is both fast and reliable. The method uses a traditional sequence alignment algorithm to generate alignments which are then evaluated by a method derived from threading techniques. As a ®nal step, each threaded model is evaluated by a neural n ..."
Abstract - Cited by 214 (10 self) - Add to MetaCart
A new protein fold recognition method is described which is both fast and reliable. The method uses a traditional sequence alignment algorithm to generate alignments which are then evaluated by a method derived from threading techniques. As a ®nal step, each threaded model is evaluated by a neural

Fast algorithms for large-scale genome alignment and comparison

by Arthur L Delcher , Adam Phillippy , Jane Carlton , Steven L Salzberg - Nucleic Acids Res , 2002
"... ABSTRACT We describe a suffix-tree algorithm that can align the entire genome sequences of eukaryotic and prokaryotic organisms with minimal use of computer time and memory. The new system, MUMmer 2, runs three times faster while using one-third as much memory as the original MUMmer system. It has ..."
Abstract - Cited by 180 (3 self) - Add to MetaCart
to both incomplete and complete genome sequences in order to detect regions of conserved synteny, in which multiple proteins from one organism are found in the same order and orientation in another. The system code is being made freely available by the authors.

RASCAL: rapid scanning and correction of multiple sequence alignments

by J. D. Thompson, J. C. Thierry, O. Poch - Bioinformatics , 2003
"... Motivation: Most multiple sequence alignment programs use heuristics that sometimes introduce errors into the alignment. The most commonly used methods to cor-rect these errors use iterative techniques to maximize an objective function. We present here an alternative, knowledge-based approach that c ..."
Abstract - Cited by 30 (5 self) - Add to MetaCart
reliable and efficient refinement strategy. Results: The accuracy and reliability of RASCAL is demonstrated using: (i) alignments from the BAliBASE benchmark database, where significant improvements were often observed, with no deterioration of the existing high-quality regions, (ii) a large scale study

Automatic recognition of regions of intrinsically poor multiple alignment using machine learning

by Yunfeng Shan, Evangelos E. Milios, Andrew J. Roger, Christian Blouin, Edward Susko - In CSB’03 , 2003
"... Phylogenetic analysis requires alignment of gene or protein sequences. Some regions of genes evolve fast and suffer numerous insertion and deletion events and cannot be aligned reliably with automatic alignment algorithms. Such regions of intrinsically uncertain alignment are currently detected and ..."
Abstract - Cited by 5 (0 self) - Add to MetaCart
Phylogenetic analysis requires alignment of gene or protein sequences. Some regions of genes evolve fast and suffer numerous insertion and deletion events and cannot be aligned reliably with automatic alignment algorithms. Such regions of intrinsically uncertain alignment are currently detected

IEPAD: Information Extraction Based on Pattern Discovery

by Chia-hui Chang, Shao-Chen Lui , 2001
"... The research in information extraction (IE) regards the generation of wrappers that can extract particular information from semistructured Web documents. Similar to compiler generation, the extractor is actually a driver program, which is accompanied with the generated extraction rule. Previous work ..."
Abstract - Cited by 139 (8 self) - Add to MetaCart
work in this field aims to learn extraction rules from users' training example. In this paper, we propose IEPAD, a system that automatically discovers extraction rules from Web pages. The system can automatically identify record boundary by repeated pattern mining and multiple sequence alignment

Touring protein fold space with DALI/FSSP

by Liisa Holm, Chris S - Nucleic Acids Res , 1998
"... The FSSP database and its new supplement, the Dali Domain Dictionary, present a continuously updated classification of all known 3D protein structures. The classification is derived using an automatic structure alignment program (Dali) for the all-against-all comparison of structures in the Protein ..."
Abstract - Cited by 188 (0 self) - Add to MetaCart
.embl-ebi.ac.uk/dali. The web interface provides a rich network of links between neighbours in fold space, between domains and proteins, and between structures and sequences leading, for example, to a database of explicit multiple alignments of protein families in the twilight zone of sequence similarity. The Dali

Multiple Lyrics Alignment: Automatic Retrieval of Song Lyrics

by Peter Knees, Markus Schedl, Gerhard Widmer , 2005
"... We present an approach to automatically retrieve and extract lyrics of arbitrary songs from the Internet. It is intended to provide easy and convenient access to lyrics for users, as well as a basis for further research based on lyrics, e.g. semantic analysis. Due to the fact that many lyrics found ..."
Abstract - Cited by 27 (6 self) - Add to MetaCart
on the web suffer from individual errors like typos, we make use of multiple versions from different sources to eliminate mistakes. This is accomplished by Multiple Sequence Alignment. The different sites are aligned and examined for matching sequences of words, finding those parts on the pages

LEON: multiple alignment evaluation of neighbours

by Julie D. Thompson, Veâronique Prigent, Olivier Poch - Nucl. Acids Res , 2004
"... Sequence alignments are fundamental to a wide range of applications, including database search-ing, functional residue identi®cation and structure prediction techniques. These applications predict or propagate structural/functional/evolutionary infor-mation based on a presumed homology between the a ..."
Abstract - Cited by 9 (1 self) - Add to MetaCart
the aligned sequences. If the initial hypothesis of homology is wrong, no subsequent application, however sophisticated, can be expected to yield accurate results. Here we present a novel method, LEON, to predict homology between proteins based on a multiple alignment of complete sequences (MACS). In MACS
Results 1 - 10 of 295