Home
Random
Nearby
Log in
Settings
Donate
About Wikidata
Disclaimers
Search
(Q33347409)
Watch
English
The effectiveness of position- and composition-specific gap costs for protein similarity searches.
scientific article
In more languages
default for all languages
No label defined
No description defined
edit
Statements
instance of
scholarly article
1 reference
stated in
Europe PubMed Central
PMC publication ID
2718649
reference URL
https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:18586708%20AND%20SRC:MED&resulttype=core&format=json
retrieved
9 January 2020
title
The effectiveness of position- and composition-specific gap costs for protein similarity searches
(English)
1 reference
stated in
Europe PubMed Central
PMC publication ID
2718649
reference URL
https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:18586708%20AND%20SRC:MED&resulttype=core&format=json
retrieved
9 January 2020
author
Aleksandar Stojmirović
series ordinal
1
1 reference
stated in
Europe PubMed Central
PMC publication ID
2718649
reference URL
https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:18586708%20AND%20SRC:MED&resulttype=core&format=json
retrieved
9 January 2020
E Michael Gertz
series ordinal
2
1 reference
stated in
Europe PubMed Central
PMC publication ID
2718649
reference URL
https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:18586708%20AND%20SRC:MED&resulttype=core&format=json
retrieved
9 January 2020
author name string
Stephen F Altschul
series ordinal
3
1 reference
stated in
Europe PubMed Central
PMC publication ID
2718649
reference URL
https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:18586708%20AND%20SRC:MED&resulttype=core&format=json
retrieved
9 January 2020
Yi-Kuo Yu
series ordinal
4
1 reference
stated in
Europe PubMed Central
PMC publication ID
2718649
reference URL
https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:18586708%20AND%20SRC:MED&resulttype=core&format=json
retrieved
9 January 2020
language of work or name
English
0 references
publication date
1 July 2008
1 reference
stated in
Europe PubMed Central
PMC publication ID
2718649
reference URL
https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:18586708%20AND%20SRC:MED&resulttype=core&format=json
retrieved
9 January 2020
published in
Bioinformatics
1 reference
stated in
Europe PubMed Central
PMC publication ID
2718649
reference URL
https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:18586708%20AND%20SRC:MED&resulttype=core&format=json
retrieved
9 January 2020
volume
24
1 reference
stated in
Europe PubMed Central
PMC publication ID
2718649
reference URL
https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:18586708%20AND%20SRC:MED&resulttype=core&format=json
retrieved
9 January 2020
issue
13
1 reference
stated in
Europe PubMed Central
PMC publication ID
2718649
reference URL
https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:18586708%20AND%20SRC:MED&resulttype=core&format=json
retrieved
9 January 2020
page(s)
i15-23
1 reference
stated in
Europe PubMed Central
PMC publication ID
2718649
reference URL
https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:18586708%20AND%20SRC:MED&resulttype=core&format=json
retrieved
9 January 2020
cites work
Data growth and its impact on the SCOP database: new developments
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=2718649
retrieved
21 June 2018
Database resources of the National Center for Biotechnology Information
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=2718649
retrieved
21 June 2018
The SUPERFAMILY database in 2007: families and functions
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=2718649
retrieved
21 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=2718649
retrieved
21 June 2018
Pfam: clans, web tools and services
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=2718649
retrieved
21 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=2718649
retrieved
21 June 2018
Improved profile HMM performance by assessment of critical algorithmic features in SAM and HMMER
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=2718649
retrieved
21 June 2018
Comparative evaluation of word composition distances for the recognition of SCOP relationships.
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=2718649
retrieved
21 June 2018
Gaps in structurally similar proteins: towards improvement of multiple sequence 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=2718649
retrieved
21 June 2018
The ASTRAL Compendium in 2004
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=2718649
retrieved
21 June 2018
The compositional adjustment of amino acid 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=2718649
retrieved
21 June 2018
Comparison of three methods for estimating the standard error of the area under the curve in ROC analysis of quantitative data
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=2718649
retrieved
21 June 2018
Empirical determination of effective gap penalties for 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=2718649
retrieved
21 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=2718649
retrieved
21 June 2018
Assignment of homology to genome sequences using a library of hidden Markov models that represent all proteins of known structure
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=2718649
retrieved
21 June 2018
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=2718649
retrieved
21 June 2018
Profile 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=2718649
retrieved
21 June 2018
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=2718649
retrieved
21 June 2018
Scoring 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=2718649
retrieved
21 June 2018
Hidden Markov models for sequence analysis: extension and analysis of the basic 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=2718649
retrieved
21 June 2018
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=2718649
retrieved
21 June 2018
SCOP: a structural classification of proteins database for the investigation of sequences and structures
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=2718649
retrieved
21 June 2018
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=2718649
retrieved
21 June 2018
The meaning and use of the area under a receiver operating characteristic (ROC) curve
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=2718649
retrieved
21 June 2018
Profile analysis: detection of distantly related proteins
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=2718649
retrieved
21 June 2018
Amino acid substitution matrices from protein blocks
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=2718649
retrieved
21 June 2018
Use of receiver operating characteristic (ROC) analysis to evaluate sequence matching
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=2718649
retrieved
31 October 2018
SSALN: an alignment algorithm using structure-dependent substitution matrices and gap penalties learned from structurally aligned protein pairs.
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=2718649
retrieved
31 October 2018
Calibrating E-values for hidden Markov models using reverse-sequence null 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=2718649
retrieved
31 October 2018
Hybrid alignment: high-performance with universal statistics.
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=2718649
retrieved
31 October 2018
Statistical significance of probabilistic sequence alignment and related local 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=2718649
retrieved
31 October 2018
Empirical and structural models for insertions and deletions in the divergent evolution of proteins.
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=2718649
retrieved
31 October 2018
An improved algorithm for matching biological sequences.
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=2718649
retrieved
31 October 2018
Analysis of insertions/deletions in protein structures
1 reference
stated in
PubMed
reference URL
https://pubmed.ncbi.nlm.nih.gov/18586708
retrieved
12 December 2020
based on heuristic
inferred from PubMed ID database lookup
Empirical analysis of protein insertions and deletions determining parameters for the correct placement of gaps in protein sequence alignments
1 reference
stated in
PubMed
reference URL
https://pubmed.ncbi.nlm.nih.gov/18586708
retrieved
12 December 2020
based on heuristic
inferred from PubMed ID database lookup
Identifiers
DOI
10.1093/BIOINFORMATICS/BTN171
1 reference
stated in
Europe PubMed Central
PMC publication ID
2718649
reference URL
https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:18586708%20AND%20SRC:MED&resulttype=core&format=json
retrieved
9 January 2020
arXiv ID
0801.2587
1 reference
stated in
Unpaywall
DBLP publication ID
conf/ismb/StojmirovicGAY08
1 reference
stated in
DBLP Dataset 2021-01-02
retrieved
28 January 2021
PMC publication ID
2718649
1 reference
stated in
Europe PubMed Central
PMC publication ID
2718649
reference URL
https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:18586708%20AND%20SRC:MED&resulttype=core&format=json
retrieved
9 January 2020
PubMed publication ID
18586708
1 reference
stated in
Europe PubMed Central
PMC publication ID
2718649
reference URL
https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:18586708%20AND%20SRC:MED&resulttype=core&format=json
retrieved
9 January 2020
ResearchGate publication ID
5268690
0 references
Sitelinks
Wikipedia
(0 entries)
edit
Wikibooks
(0 entries)
edit
Wikinews
(0 entries)
edit
Wikiquote
(0 entries)
edit
Wikisource
(0 entries)
edit
Wikiversity
(0 entries)
edit
Wikivoyage
(0 entries)
edit
Wiktionary
(0 entries)
edit
Multilingual sites
(0 entries)
edit