Substitution matrix (English Wikipedia)

Analysis of information sources in references of the Wikipedia article "Substitution matrix" in English language version.

refsWebsite

Global rank English rank

14nih.gov

4^th place

13doi.org

2^nd place

2semanticscholar.org

11^th place

8^th place

1cambridge.org

305^th place

264^th place

1worldcat.org

5^th place

1iqtree.github.io

low place

1github.com

383^rd place

320^th place

1h-its.org

low place

1psu.edu

207^th place

136^th place

1harvard.edu

18^th place

17^th place

cambridge.org

ebooks.cambridge.org

Xiong, Jin (2006). Essential Bioinformatics. Cambridge: Cambridge University Press. doi:10.1017/cbo9780511806087.004. ISBN 978-0-511-80608-7.

doi.org

Xiong, Jin (2006). Essential Bioinformatics. Cambridge: Cambridge University Press. doi:10.1017/cbo9780511806087.004. ISBN 978-0-511-80608-7.
Styczynski, Mark P; Jensen, Kyle L; Rigoutsos, Isidore; Stephanopoulos, Gregory (March 2008). "BLOSUM62 miscalculations improve search performance". Nature Biotechnology. 26 (3): 274–275. doi:10.1038/nbt0308-274. PMID 18327232. S2CID 205266180.
Whelan, Simon; Goldman, Nick (1 May 2001). "A General Empirical Model of Protein Evolution Derived from Multiple Protein Families Using a Maximum-Likelihood Approach". Molecular Biology and Evolution. 18 (5): 691–699. doi:10.1093/oxfordjournals.molbev.a003851. ISSN 0737-4038. PMID 11319253.
Trivedi, R; Nagarajaram, HA (November 2020). "Substitution scoring matrices for proteins - An overview". Protein Science. 29 (11): 2150–2163. doi:10.1002/pro.3954. PMC 7586916. PMID 32954566.
Veerassamy, Shalini; Smith, Andrew; Tillier, Elisabeth R. M. (December 2003). "A Transition Probability Model for Amino Acid Substitutions from Blocks". Journal of Computational Biology. 10 (6): 997–1010. doi:10.1089/106652703322756195. PMID 14980022.
Le, S. Q.; Gascuel, O. (3 April 2008). "An Improved General Amino Acid Replacement Matrix". Molecular Biology and Evolution. 25 (7): 1307–1320. doi:10.1093/molbev/msn067. PMID 18367465.
Minh, Bui Quang; Dang, Cuong Cao; Vinh, Le Sy; Lanfear, Robert (11 August 2021). "QMaker: Fast and Accurate Method to Estimate Empirical Models of Protein Evolution". Systematic Biology. 70 (5): 1046–1060. doi:10.1093/sysbio/syab010.
Dang, Cuong Cao; Minh, Bui Quang; McShea, Hanon; Masel, Joanna; James, Jennifer Eleanor; Vinh, Le Sy; Lanfear, Robert (10 August 2022). "nQMaker: Estimating Time Nonreversible Amino Acid Substitution Models". Systematic Biology. 71 (5): 1110–1123. doi:10.1093/sysbio/syac007. PMC 9366462. PMID 35139203.
Müller, T; Rahmann, S; Rehmsmeier, M (2001). "Non-symmetric score matrices and the detection of homologous transmembrane proteins". Bioinformatics. 17 (Suppl 1): S182–9. doi:10.1093/bioinformatics/17.suppl_1.s182. PMID 11473008.
Rice, DW; Eisenberg, D (1997). "A 3D-1D substitution matrix for protein fold recognition that includes predicted secondary structure of the sequence". Journal of Molecular Biology. 267 (4): 1026–38. CiteSeerX 10.1.1.44.1143. doi:10.1006/jmbi.1997.0924. PMID 9135128.
Gong, Sungsam; Blundell, Tom L. (2008). Levitt, Michael (ed.). "Discarding functional residues from the substitution table improves predictions of active sites within three-dimensional structures". PLOS Computational Biology. 4 (10): e1000179. Bibcode:2008PLSCB...4E0179G. doi:10.1371/journal.pcbi.1000179. PMC 2527532. PMID 18833291.
Goonesekere, NC; Lee, B (2008). "Context-specific amino acid substitution matrices and their use in the detection of protein homologs". Proteins. 71 (2): 910–9. doi:10.1002/prot.21775. PMID 18004781. S2CID 27443393.
Huang, YM; Bystroff, C (2006). "Improved pairwise alignments of proteins in the Twilight Zone using local structure predictions". Bioinformatics. 22 (4): 413–22. doi:10.1093/bioinformatics/bti828. PMID 16352653.

github.com

"phyml/doc/phyml-manual.pdf at master · stephaneguindon/phyml" (PDF). GitHub.

h-its.org

cme.h-its.org

Stamatakis, Alexandros (July 20, 2016). "The RAxML v8.2.X Manual" (PDF).

harvard.edu

ui.adsabs.harvard.edu

Gong, Sungsam; Blundell, Tom L. (2008). Levitt, Michael (ed.). "Discarding functional residues from the substitution table improves predictions of active sites within three-dimensional structures". PLOS Computational Biology. 4 (10): e1000179. Bibcode:2008PLSCB...4E0179G. doi:10.1371/journal.pcbi.1000179. PMC 2527532. PMID 18833291.

iqtree.github.io

"Substitution Models". iqtree.github.io.

nih.gov

pubmed.ncbi.nlm.nih.gov

Styczynski, Mark P; Jensen, Kyle L; Rigoutsos, Isidore; Stephanopoulos, Gregory (March 2008). "BLOSUM62 miscalculations improve search performance". Nature Biotechnology. 26 (3): 274–275. doi:10.1038/nbt0308-274. PMID 18327232. S2CID 205266180.
Whelan, Simon; Goldman, Nick (1 May 2001). "A General Empirical Model of Protein Evolution Derived from Multiple Protein Families Using a Maximum-Likelihood Approach". Molecular Biology and Evolution. 18 (5): 691–699. doi:10.1093/oxfordjournals.molbev.a003851. ISSN 0737-4038. PMID 11319253.
Trivedi, R; Nagarajaram, HA (November 2020). "Substitution scoring matrices for proteins - An overview". Protein Science. 29 (11): 2150–2163. doi:10.1002/pro.3954. PMC 7586916. PMID 32954566.
Veerassamy, Shalini; Smith, Andrew; Tillier, Elisabeth R. M. (December 2003). "A Transition Probability Model for Amino Acid Substitutions from Blocks". Journal of Computational Biology. 10 (6): 997–1010. doi:10.1089/106652703322756195. PMID 14980022.
Le, S. Q.; Gascuel, O. (3 April 2008). "An Improved General Amino Acid Replacement Matrix". Molecular Biology and Evolution. 25 (7): 1307–1320. doi:10.1093/molbev/msn067. PMID 18367465.
Dang, Cuong Cao; Minh, Bui Quang; McShea, Hanon; Masel, Joanna; James, Jennifer Eleanor; Vinh, Le Sy; Lanfear, Robert (10 August 2022). "nQMaker: Estimating Time Nonreversible Amino Acid Substitution Models". Systematic Biology. 71 (5): 1110–1123. doi:10.1093/sysbio/syac007. PMC 9366462. PMID 35139203.
Müller, T; Rahmann, S; Rehmsmeier, M (2001). "Non-symmetric score matrices and the detection of homologous transmembrane proteins". Bioinformatics. 17 (Suppl 1): S182–9. doi:10.1093/bioinformatics/17.suppl_1.s182. PMID 11473008.
Rice, DW; Eisenberg, D (1997). "A 3D-1D substitution matrix for protein fold recognition that includes predicted secondary structure of the sequence". Journal of Molecular Biology. 267 (4): 1026–38. CiteSeerX 10.1.1.44.1143. doi:10.1006/jmbi.1997.0924. PMID 9135128.
Gong, Sungsam; Blundell, Tom L. (2008). Levitt, Michael (ed.). "Discarding functional residues from the substitution table improves predictions of active sites within three-dimensional structures". PLOS Computational Biology. 4 (10): e1000179. Bibcode:2008PLSCB...4E0179G. doi:10.1371/journal.pcbi.1000179. PMC 2527532. PMID 18833291.
Goonesekere, NC; Lee, B (2008). "Context-specific amino acid substitution matrices and their use in the detection of protein homologs". Proteins. 71 (2): 910–9. doi:10.1002/prot.21775. PMID 18004781. S2CID 27443393.
Huang, YM; Bystroff, C (2006). "Improved pairwise alignments of proteins in the Twilight Zone using local structure predictions". Bioinformatics. 22 (4): 413–22. doi:10.1093/bioinformatics/bti828. PMID 16352653.

ncbi.nlm.nih.gov

Trivedi, R; Nagarajaram, HA (November 2020). "Substitution scoring matrices for proteins - An overview". Protein Science. 29 (11): 2150–2163. doi:10.1002/pro.3954. PMC 7586916. PMID 32954566.
Dang, Cuong Cao; Minh, Bui Quang; McShea, Hanon; Masel, Joanna; James, Jennifer Eleanor; Vinh, Le Sy; Lanfear, Robert (10 August 2022). "nQMaker: Estimating Time Nonreversible Amino Acid Substitution Models". Systematic Biology. 71 (5): 1110–1123. doi:10.1093/sysbio/syac007. PMC 9366462. PMID 35139203.
Gong, Sungsam; Blundell, Tom L. (2008). Levitt, Michael (ed.). "Discarding functional residues from the substitution table improves predictions of active sites within three-dimensional structures". PLOS Computational Biology. 4 (10): e1000179. Bibcode:2008PLSCB...4E0179G. doi:10.1371/journal.pcbi.1000179. PMC 2527532. PMID 18833291.

psu.edu

citeseerx.ist.psu.edu

Rice, DW; Eisenberg, D (1997). "A 3D-1D substitution matrix for protein fold recognition that includes predicted secondary structure of the sequence". Journal of Molecular Biology. 267 (4): 1026–38. CiteSeerX 10.1.1.44.1143. doi:10.1006/jmbi.1997.0924. PMID 9135128.

semanticscholar.org

api.semanticscholar.org

Styczynski, Mark P; Jensen, Kyle L; Rigoutsos, Isidore; Stephanopoulos, Gregory (March 2008). "BLOSUM62 miscalculations improve search performance". Nature Biotechnology. 26 (3): 274–275. doi:10.1038/nbt0308-274. PMID 18327232. S2CID 205266180.
Goonesekere, NC; Lee, B (2008). "Context-specific amino acid substitution matrices and their use in the detection of protein homologs". Proteins. 71 (2): 910–9. doi:10.1002/prot.21775. PMID 18004781. S2CID 27443393.

worldcat.org

search.worldcat.org

Whelan, Simon; Goldman, Nick (1 May 2001). "A General Empirical Model of Protein Evolution Derived from Multiple Protein Families Using a Maximum-Likelihood Approach". Molecular Biology and Evolution. 18 (5): 691–699. doi:10.1093/oxfordjournals.molbev.a003851. ISSN 0737-4038. PMID 11319253.