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Accelerated Profile HMM Searches
scientific article (publication date: October 2011)
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title
Accelerated Profile HMM Searches
(English)
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PubMed
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=pubmed&retmode=json&id=22039361
retrieved
23 April 2017
author
Sean Eddy
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Sean R Eddy
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23 April 2017
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=pubmed&retmode=json&id=22039361
language of work or name
English
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PubMed
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=pubmed&retmode=json&id=22039361
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23 April 2017
publication date
October 2011
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PubMed
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=pubmed&retmode=json&id=22039361
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23 April 2017
published in
PLOS Computational Biology
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PubMed
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=pubmed&retmode=json&id=22039361
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23 April 2017
volume
7
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23 April 2017
issue
10
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23 April 2017
page(s)
e1002195
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23 April 2017
copyright license
Creative Commons Attribution 4.0 International
start time
20 October 2011
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April 2022 Public Data File from Crossref
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copyrighted
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cites work
Ongoing and future developments at the Universal Protein Resource
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=3197634
retrieved
23 April 2017
BLAST+: architecture and applications
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=3197634
retrieved
23 April 2017
The Pfam protein families database
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=3197634
retrieved
23 April 2017
InterPro: the integrative protein signature database
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=3197634
retrieved
23 April 2017
A probabilistic model of local sequence alignment that simplifies statistical significance estimation
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=3197634
retrieved
23 April 2017
Exploring genomic dark matter: a critical assessment of the performance of homology search methods on noncoding RNA
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=3197634
retrieved
23 April 2017
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
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=3197634
retrieved
23 April 2017
Identification of common molecular subsequences
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=3197634
retrieved
23 April 2017
Basic local alignment search tool
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=3197634
retrieved
23 April 2017
Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements
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=3197634
retrieved
23 April 2017
Flexible sequence similarity searching with the FASTA3 program package
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=3197634
retrieved
23 April 2017
Hidden Markov models for detecting remote protein homologies
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=3197634
retrieved
23 April 2017
Hidden Markov models in computational biology. Applications to protein modeling
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=3197634
retrieved
23 April 2017
Hidden Markov model speed heuristic and iterative HMM search procedure
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=3197634
retrieved
3 June 2018
Composition-based statistics and translated nucleotide searches: improving the TBLASTN module of BLAST
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=3197634
retrieved
3 June 2018
Striped Smith-Waterman speeds database searches six times over other SIMD implementations
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=3197634
retrieved
3 June 2018
Retrieval accuracy, statistical significance and compositional similarity in protein sequence database searches
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=3197634
retrieved
3 June 2018
Protein database searches using compositionally adjusted substitution matrices
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=3197634
retrieved
3 June 2018
Statistical evaluation of pairwise protein sequence comparison with the Bayesian bootstrap
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=3197634
retrieved
3 June 2018
SledgeHMMER: a web server for batch searching the Pfam database
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=3197634
retrieved
3 June 2018
A comparison of profile hidden Markov model procedures for remote homology detection
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=3197634
retrieved
3 June 2018
ParAlign: a parallel sequence alignment algorithm for rapid and sensitive database searches.
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=3197634
retrieved
3 June 2018
The estimation of statistical parameters for local alignment score distributions.
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=3197634
retrieved
3 June 2018
Homology detection via family pairwise search
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=3197634
retrieved
3 June 2018
Using video-oriented instructions to speed up sequence comparison
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=3197634
retrieved
3 June 2018
Designing patterns and profiles for faster HMM search
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=3197634
retrieved
26 November 2018
Designing patterns for profile HMM search
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=3197634
retrieved
26 November 2018
Six-fold speed-up of Smith-Waterman sequence database searches using parallel processing on common microprocessors
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=3197634
retrieved
26 November 2018
Discovering simple DNA sequences by the algorithmic significance method.
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=3197634
retrieved
26 November 2018
Identifiers
DOI
10.1371/JOURNAL.PCBI.1002195
2 references
stated in
PubMed
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=pubmed&retmode=json&id=22039361
retrieved
23 April 2017
stated in
Consolidated OpenCitations Corpus – April 2017
OpenCitations bibliographic resource ID
151202
DBLP publication ID
journals/ploscb/Eddy11
1 reference
stated in
DBLP Dataset 2021-01-02
retrieved
28 January 2021
OpenCitations bibliographic resource ID
151202
1 reference
stated in
Consolidated OpenCitations Corpus – April 2017
OpenCitations bibliographic resource ID
151202
PMC publication ID
3197634
2 references
stated in
PubMed
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=pubmed&retmode=json&id=22039361
retrieved
23 April 2017
stated in
Consolidated OpenCitations Corpus – April 2017
OpenCitations bibliographic resource ID
151202
PubMed publication ID
22039361
2 references
stated in
PubMed
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=pubmed&retmode=json&id=22039361
retrieved
23 April 2017
stated in
Consolidated OpenCitations Corpus – April 2017
OpenCitations bibliographic resource ID
151202
ResearchGate publication ID
51753930
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Semantic Scholar paper ID
9835596dff5dd7a2f9fcaedf478adbb2a34ca0a5
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