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Homology-extended sequence alignment
scientific article
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Statements
instance of
scholarly article
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title
Homology-extended sequence alignment
(English)
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main subject
sequence alignment
1 reference
based on heuristic
inferred from title
author
Jaap Heringa
series ordinal
3
object named as
J Heringa
0 references
Jens Kleinjung
object named as
J Kleinjung
series ordinal
2
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author name string
V A Simossis
series ordinal
1
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J Heringa
series ordinal
3
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language of work or name
English
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publication date
2005
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published in
Nucleic Acids Research
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volume
33
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issue
3
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page(s)
816-24
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cites work
Protein family comparison using statistical models and predicted structural information
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PubMed Central
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MUSCLE: multiple sequence alignment with high accuracy and high throughput
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Profile-profile comparisons by COMPASS predict intricate homologies between protein families
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PubMed Central
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Improving the quality of twilight-zone alignments
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PubMed Central
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Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
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7 April 2017
CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
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7 April 2017
The relation between the divergence of sequence and structure in proteins
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PubMed Central
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7 April 2017
Amino acid substitution matrices from protein blocks
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PubMed Central
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7 April 2017
T-Coffee: A novel method for fast and accurate multiple sequence alignment
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7 April 2017
Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features
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PubMed Central
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7 April 2017
A general method applicable to the search for similarities in the amino acid sequence of two proteins
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=549400
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7 April 2017
The rapid generation of mutation data matrices from protein sequences
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7 April 2017
HOMSTRAD: a database of protein structure alignments for homologous families
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PubMed Central
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7 April 2017
Exhaustive matching of the entire protein sequence database
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PubMed Central
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7 April 2017
Twilight zone of protein sequence alignments
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=549400
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7 April 2017
Iterated profile searches with PSI-BLAST--a tool for discovery in protein databases
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PubMed Central
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7 April 2017
Progressive sequence alignment as a prerequisite to correct phylogenetic trees
1 reference
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=549400
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7 April 2017
Detecting distant homology with Meta-BASIC.
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=549400
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28 September 2017
Contact-based sequence alignment
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=549400
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28 September 2017
Arby: automatic protein structure prediction using profile-profile alignment and confidence measures.
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=549400
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28 September 2017
HOMSTRAD: recent developments of the Homologous Protein Structure Alignment Database.
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=549400
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28 September 2017
The compositional adjustment of amino acid substitution matrices
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28 September 2017
ORFeus: Detection of distant homology using sequence profiles and predicted secondary structure
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=549400
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28 September 2017
Profile-profile alignment: a powerful tool for protein structure prediction.
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=549400
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28 September 2017
Computational methods for protein secondary structure prediction using multiple sequence alignments
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PubMed Central
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28 September 2017
BAliBASE (Benchmark Alignment dataBASE): enhancements for repeats, transmembrane sequences and circular permutations
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PubMed Central
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28 September 2017
DbClustal: rapid and reliable global multiple alignments of protein sequences detected by database searches
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=549400
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28 September 2017
IMPALA: matching a protein sequence against a collection of PSI-BLAST-constructed position-specific score matrices
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28 September 2017
Scoring profile-to-profile sequence alignments
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PubMed Central
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A comparison of scoring functions for protein sequence profile alignment
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=549400
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30 May 2018
Comparison of sequence profiles. Strategies for structural predictions using sequence information
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PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=549400
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30 May 2018
Dynamic sequence databank searching with templates and multiple alignment
1 reference
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PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=549400
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30 May 2018
A comprehensive examination of protein sequences for evidence of internal gene duplication
1 reference
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PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=549400
retrieved
30 May 2018
Profile-profile methods provide improved fold-recognition: A study of different profile-profile alignment methods
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=549400
retrieved
28 November 2018
COACH: profile-profile alignment of protein families using hidden Markov models
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=549400
retrieved
28 November 2018
FORTE: a profile-profile comparison tool for protein fold recognition.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=549400
retrieved
28 November 2018
A Shannon entropy-based filter detects high- quality profile-profile alignments in searches for remote homologues.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=549400
retrieved
28 November 2018
The PRALINE online server: optimising progressive multiple alignment on the web.
1 reference
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PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=549400
retrieved
28 November 2018
Probabilistic scoring measures for profile-profile comparison yield more accurate short seed alignments
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=549400
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28 November 2018
Testing homology with Contact Accepted mutatiOn (CAO): a contact-based Markov model of protein evolution.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=549400
retrieved
28 November 2018
PCMA: fast and accurate multiple sequence alignment based on profile consistency.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=549400
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28 November 2018
Parallelized multiple alignment.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=549400
retrieved
28 November 2018
Within the twilight zone: a sensitive profile-profile comparison tool based on information theory.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=549400
retrieved
28 November 2018
Iterated sequence databank search methods.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=549400
retrieved
28 November 2018
Two strategies for sequence comparison: profile-preprocessed and secondary structure-induced multiple alignment.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=549400
retrieved
28 November 2018
Modeling amino acid replacement
1 reference
stated in
PubMed
reference URL
https://pubmed.ncbi.nlm.nih.gov/15699183
retrieved
12 December 2020
based on heuristic
inferred from PubMed ID database lookup
Estimating amino acid substitution models: a comparison of Dayhoff's estimator, the resolvent approach and a maximum likelihood method
1 reference
stated in
PubMed
reference URL
https://pubmed.ncbi.nlm.nih.gov/15699183
retrieved
12 December 2020
based on heuristic
inferred from PubMed ID database lookup
COMPASS: a tool for comparison of multiple protein alignments with assessment of statistical significance
1 reference
stated in
PubMed
reference URL
https://pubmed.ncbi.nlm.nih.gov/15699183
retrieved
12 December 2020
based on heuristic
inferred from PubMed ID database lookup
Identifiers
DOI
10.1093/NAR/GKI233
1 reference
stated in
Consolidated OpenCitations Corpus – April 2017
OpenCitations bibliographic resource ID
3907911
OpenCitations bibliographic resource ID
3907911
1 reference
stated in
Consolidated OpenCitations Corpus – April 2017
OpenCitations bibliographic resource ID
3907911
PMC publication ID
549400
1 reference
stated in
Consolidated OpenCitations Corpus – April 2017
OpenCitations bibliographic resource ID
3907911
PubMed publication ID
15699183
1 reference
stated in
Consolidated OpenCitations Corpus – April 2017
OpenCitations bibliographic resource ID
3907911
ResearchGate publication ID
8033888
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