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Twilight Zone of Protein Sequence Alignments
, 1999
"... l findings are applicable to automatic database searches. Keywords: alignment quality analysis/evolutionary conservation/ genome analysis/protein sequence alignment/sequence space hopping Introduction Protein sequence alignments in twilight zone Protein sequences fold into unique three-dimension ..."
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Cited by 397 (49 self)
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l findings are applicable to automatic database searches. Keywords: alignment quality analysis/evolutionary conservation/ genome analysis/protein sequence alignment/sequence space hopping Introduction Protein sequence alignments in twilight zone Protein sequences fold into unique three
The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000
- Nucleic Acids Res
, 2000
"... SWISS-PROT is a curated protein sequence database which strives to provide a high level of annotation (such as the description of the function of a protein, its domains structure, post-translational modifications, variants, etc.), a minimal level of redundancy and high level of integration with othe ..."
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Cited by 773 (21 self)
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SWISS-PROT is a curated protein sequence database which strives to provide a high level of annotation (such as the description of the function of a protein, its domains structure, post-translational modifications, variants, etc.), a minimal level of redundancy and high level of integration
The SWISS-PROT protein sequence data bank and its supplement TrEMBL in 1999
- Nucleic Acids Res
, 1999
"... SWISS-PROT is a curated protein sequence database which strives to provide a high level of annotation (such as the description of the function of a protein, its domain structure, post-translational modifications, variants, etc.), a minimal level of redundancy and high level of integration with other ..."
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Cited by 624 (5 self)
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SWISS-PROT is a curated protein sequence database which strives to provide a high level of annotation (such as the description of the function of a protein, its domain structure, post-translational modifications, variants, etc.), a minimal level of redundancy and high level of integration
MIPS: a database for genomes and protein sequences
- Nucleic Acids Res
, 2002
"... The Munich Information Center for Protein Sequences (MIPS-GSF, Neuherberg, Germany) continues to provide genome-related information in a systematic way. MIPS supports both national and European sequencing and functional analysis projects, develops and maintains automatically generated and manually a ..."
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Cited by 336 (10 self)
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The Munich Information Center for Protein Sequences (MIPS-GSF, Neuherberg, Germany) continues to provide genome-related information in a systematic way. MIPS supports both national and European sequencing and functional analysis projects, develops and maintains automatically generated and manually
A hidden Markov model for predicting transmembrane helices in protein sequences
- In Proceedings of the 6th International Conference on Intelligent Systems for Molecular Biology (ISMB
, 1998
"... A novel method to model and predict the location and orientation of alpha helices in membrane- spanning proteins is presented. It is based on a hidden Markov model (HMM) with an architecture that corresponds closely to the biological system. The model is cyclic with 7 types of states for helix core, ..."
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Cited by 373 (9 self)
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A novel method to model and predict the location and orientation of alpha helices in membrane- spanning proteins is presented. It is based on a hidden Markov model (HMM) with an architecture that corresponds closely to the biological system. The model is cyclic with 7 types of states for helix core
Multiple sequence alignment with the Clustal series of programs
- 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 ..."
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Cited by 747 (5 self)
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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
Sequence Logos: A New Way to Display Consensus Sequences
- 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. ..."
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Cited by 650 (28 self)
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. The relative frequencies of every residue at every position. 4. The amount of information present at every position in the sequence, measured in bits. 5. An initiation point, cut point, or other significant location (if appropriate) . Any aligned set of DNA, RNA or protein sequences can be represented using
Muscle: multiple sequence alignment with high accuracy and high throughput
- 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 ..."
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Cited by 2509 (7 self)
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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
SCOP: a structural classification of proteins database for the investigation of sequences and structures.
- J. Mol. Biol.
, 1995
"... ABSTRACT The Structural Classification of Proteins (SCOP) database provides a detailed and comprehensive description of the relationships of all known proteins structures. The classification is on hierarchical levels: the first two levels, family and superfamily, describe near and far evolutionary ..."
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Cited by 1552 (24 self)
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relationships; the third, fold, describes geometrical relationships. The distinction between evolutionary relationships and those that arise from the physics and chemistry of proteins is a feature that is unique to this database, so far. The database can be used as a source of data to calibrate sequence search
NCBI reference sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins
- NUCLEIC ACIDS RES
, 2005
"... ..."
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