List of software to detect low complexity regions in proteins (English Wikipedia)

Analysis of information sources in references of the Wikipedia article "List of software to detect low complexity regions in proteins" in English language version.

refsWebsite

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27nih.gov

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20doi.org

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4worldcat.org

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1harvard.edu

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1semanticscholar.org

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doi.org

Brendel V, Bucher P, Nourbakhsh IR, Blaisdell BE, Karlin S (15 Mar 1992). "Methods and algorithms for statistical analysis of protein sequences". Proc Natl Acad Sci U S A. 89 (6): 2002–2006. Bibcode:1992PNAS...89.2002B. doi:10.1073/pnas.89.6.2002. PMC 48584. PMID 1549558.
Wootton JC, Federhen S (June 2003). "Statistics of local complexity in amino acid sequences and sequence databases". Computers and Chemistry. 17 (2): 149–163. doi:10.1016/0097-8485(93)85006-X.
Harrison PM (13 Nov 2017). "fLPS: Fast discovery of compositional biases for the protein universe". BMC Bioinformatics. 18 (1): 476. doi:10.1186/s12859-017-1906-3. PMC 5684748. PMID 29132292.
Promponas VJ, Enright AJ, Tsoka S, Kreil DP, Leroy C, Hamodrakas S, Sander C, Ouzounis CA (Oct 2000). "CAST: an iterative algorithm for the complexity analysis of sequence tracts". Bioinformatics. 16 (10): 915–922. doi:10.1093/bioinformatics/16.10.915. PMID 11120681.
Albà MM, Laskowski RA, Hancock JM (May 2002). "Detecting cryptically simple protein sequences using the SIMPLE algorithm". Bioinformatics. 18 (5): 672–678. doi:10.1093/bioinformatics/18.5.672. PMID 12050063.
Wise MJ (2001). "0j.py: a software tool for low complexity proteins and protein domains". Bioinformatics. 17 (Suppl 1): S288 – S295. doi:10.1093/bioinformatics/17.suppl_1.s288. PMID 11473020.
Wan H, Li L, Federhen S, Wootton JC (2003). "Discovering simple regions in biological sequences associated with scoring schemes". J Comput Biol. 10 (2): 171–185. doi:10.1089/106652703321825955. PMID 12804090.
Nandi T, Dash D, Ghai R, B-Rao C, Kannan K, Brahmachari SK, Ramakrishnan C, Ramachandran S (2003). "A new algorithm for detecting low-complexity regions in protein sequences". J Biomol Struct Dyn. 20 (5): 657–668. doi:10.1080/07391102.2003.10506882. PMID 12643768. S2CID 45635217.
Shin SW, Kim SM (15 Jan 2005). "A novel complexity measure for comparative analysis of protein sequences from complete genomes". Bioinformatics. 21 (2): 160–170. doi:10.1093/bioinformatics/bth497. PMID 15333459.
Kuznetsov IB, Hwang S (1 May 2006). "A novel sensitive method for the detection of user-defined compositional bias in biological sequences". Bioinformatics. 22 (9): 1055–1063. doi:10.1093/bioinformatics/btl049. PMID 16500936.
Li X, Kahveci T (15 Dec 2006). "A Novel algorithm for identifying low-complexity regions in a protein sequence". Bioinformatics. 22 (24): 2980–2987. doi:10.1093/bioinformatics/btl495. PMID 17018537.
He D, Parkinson J (1 Apr 2008). "SubSeqer: a graph-based approach for the detection and identification of repetitive elements in low-complexity sequences". Bioinformatics. 24 (7): 1016–1017. doi:10.1093/bioinformatics/btn073. PMID 18304932.
Ooi HS, Kwo CY, Wildpaner M, Sirota FL, Eisenhaber B, Maurer-Stroh S, Wong WC, Schleiffer A, Eisenhaber F, Schneider G (Jul 2009). "ANNIE: integrated de novo protein sequence annotation". Nucleic Acids Res. 37 (Web server issue): W435 – W440. doi:10.1093/nar/gkp254. PMC 2703921. PMID 19389726.
Harbi D, Kumar M, Harrison PM (6 Jan 2011). "LPS-annotate: complete annotation of compositionally biased regions in the protein knowledgebase". Database (Oxford). 2011: baq031. doi:10.1093/database/baq031. PMC 3017391. PMID 21216786.
Kirmitzoglou I, Promponas VJ (1 Jul 2015). "LCR-eXXXplorer: a web platform to search, visualize and share data for low complexity regions in protein sequences". Bioinformatics. 31 (13): 2208–2210. doi:10.1093/bioinformatics/btv115. PMC 4481844. PMID 25712690.
Claverie JM, States D (June 1993). "Information enhancement methods for large scale sequence analysis". Computers Chem. 17 (2): 191–201. doi:10.1016/0097-8485(93)85010-a.
Silva JM, Qi W, Pinho AJ, Pratas D (2022-12-28). "AlcoR: alignment-free simulation, mapping, and visualization of low-complexity regions in biological data". GigaScience. 12. doi:10.1093/gigascience/giad101. ISSN 2047-217X. PMC 10716826. PMID 38091509.
Mier P, Paladin L, Tamana S, Petrosian S, Hajdu-Soltész B, Urbanek A, Gruca A, Plewczynski D, Grynberg M, Bernadó P, Gáspári Z (2020-03-23). "Disentangling the complexity of low complexity proteins". Briefings in Bioinformatics. 21 (2): 458–472. doi:10.1093/bib/bbz007. ISSN 1467-5463. PMC 7299295. PMID 30698641.
Jarnot P, Ziemska-Legiecka J, Dobson L, Merski M, Mier P, Andrade-Navarro MA, Hancock JM, Dosztányi Z, Paladin L, Necci M, Piovesan D (2020-07-02). "PlaToLoCo: the first web meta-server for visualization and annotation of low complexity regions in proteins". Nucleic Acids Research. 48 (W1): W77 – W84. doi:10.1093/nar/gkaa339. ISSN 0305-1048. PMC 7319588. PMID 32421769.
Ntountoumi C, Vlastaridis P, Mossialos D, Stathopoulos C, Iliopoulos I, Promponas V, Oliver SG, Amoutzias GD (2019-11-04). "Low complexity regions in the proteins of prokaryotes perform important functional roles and are highly conserved". Nucleic Acids Research. 47 (19): 9998–10009. doi:10.1093/nar/gkz730. ISSN 0305-1048. PMC 6821194. PMID 31504783.

harvard.edu

ui.adsabs.harvard.edu

Brendel V, Bucher P, Nourbakhsh IR, Blaisdell BE, Karlin S (15 Mar 1992). "Methods and algorithms for statistical analysis of protein sequences". Proc Natl Acad Sci U S A. 89 (6): 2002–2006. Bibcode:1992PNAS...89.2002B. doi:10.1073/pnas.89.6.2002. PMC 48584. PMID 1549558.

nih.gov

pubmed.ncbi.nlm.nih.gov

Brendel V, Bucher P, Nourbakhsh IR, Blaisdell BE, Karlin S (15 Mar 1992). "Methods and algorithms for statistical analysis of protein sequences". Proc Natl Acad Sci U S A. 89 (6): 2002–2006. Bibcode:1992PNAS...89.2002B. doi:10.1073/pnas.89.6.2002. PMC 48584. PMID 1549558.
Harrison PM (13 Nov 2017). "fLPS: Fast discovery of compositional biases for the protein universe". BMC Bioinformatics. 18 (1): 476. doi:10.1186/s12859-017-1906-3. PMC 5684748. PMID 29132292.
Promponas VJ, Enright AJ, Tsoka S, Kreil DP, Leroy C, Hamodrakas S, Sander C, Ouzounis CA (Oct 2000). "CAST: an iterative algorithm for the complexity analysis of sequence tracts". Bioinformatics. 16 (10): 915–922. doi:10.1093/bioinformatics/16.10.915. PMID 11120681.
Albà MM, Laskowski RA, Hancock JM (May 2002). "Detecting cryptically simple protein sequences using the SIMPLE algorithm". Bioinformatics. 18 (5): 672–678. doi:10.1093/bioinformatics/18.5.672. PMID 12050063.
Wise MJ (2001). "0j.py: a software tool for low complexity proteins and protein domains". Bioinformatics. 17 (Suppl 1): S288 – S295. doi:10.1093/bioinformatics/17.suppl_1.s288. PMID 11473020.
Wan H, Li L, Federhen S, Wootton JC (2003). "Discovering simple regions in biological sequences associated with scoring schemes". J Comput Biol. 10 (2): 171–185. doi:10.1089/106652703321825955. PMID 12804090.
Nandi T, Dash D, Ghai R, B-Rao C, Kannan K, Brahmachari SK, Ramakrishnan C, Ramachandran S (2003). "A new algorithm for detecting low-complexity regions in protein sequences". J Biomol Struct Dyn. 20 (5): 657–668. doi:10.1080/07391102.2003.10506882. PMID 12643768. S2CID 45635217.
Shin SW, Kim SM (15 Jan 2005). "A novel complexity measure for comparative analysis of protein sequences from complete genomes". Bioinformatics. 21 (2): 160–170. doi:10.1093/bioinformatics/bth497. PMID 15333459.
Kuznetsov IB, Hwang S (1 May 2006). "A novel sensitive method for the detection of user-defined compositional bias in biological sequences". Bioinformatics. 22 (9): 1055–1063. doi:10.1093/bioinformatics/btl049. PMID 16500936.
Li X, Kahveci T (15 Dec 2006). "A Novel algorithm for identifying low-complexity regions in a protein sequence". Bioinformatics. 22 (24): 2980–2987. doi:10.1093/bioinformatics/btl495. PMID 17018537.
He D, Parkinson J (1 Apr 2008). "SubSeqer: a graph-based approach for the detection and identification of repetitive elements in low-complexity sequences". Bioinformatics. 24 (7): 1016–1017. doi:10.1093/bioinformatics/btn073. PMID 18304932.
Ooi HS, Kwo CY, Wildpaner M, Sirota FL, Eisenhaber B, Maurer-Stroh S, Wong WC, Schleiffer A, Eisenhaber F, Schneider G (Jul 2009). "ANNIE: integrated de novo protein sequence annotation". Nucleic Acids Res. 37 (Web server issue): W435 – W440. doi:10.1093/nar/gkp254. PMC 2703921. PMID 19389726.
Harbi D, Kumar M, Harrison PM (6 Jan 2011). "LPS-annotate: complete annotation of compositionally biased regions in the protein knowledgebase". Database (Oxford). 2011: baq031. doi:10.1093/database/baq031. PMC 3017391. PMID 21216786.
Kirmitzoglou I, Promponas VJ (1 Jul 2015). "LCR-eXXXplorer: a web platform to search, visualize and share data for low complexity regions in protein sequences". Bioinformatics. 31 (13): 2208–2210. doi:10.1093/bioinformatics/btv115. PMC 4481844. PMID 25712690.
Silva JM, Qi W, Pinho AJ, Pratas D (2022-12-28). "AlcoR: alignment-free simulation, mapping, and visualization of low-complexity regions in biological data". GigaScience. 12. doi:10.1093/gigascience/giad101. ISSN 2047-217X. PMC 10716826. PMID 38091509.
Mier P, Paladin L, Tamana S, Petrosian S, Hajdu-Soltész B, Urbanek A, Gruca A, Plewczynski D, Grynberg M, Bernadó P, Gáspári Z (2020-03-23). "Disentangling the complexity of low complexity proteins". Briefings in Bioinformatics. 21 (2): 458–472. doi:10.1093/bib/bbz007. ISSN 1467-5463. PMC 7299295. PMID 30698641.
Jarnot P, Ziemska-Legiecka J, Dobson L, Merski M, Mier P, Andrade-Navarro MA, Hancock JM, Dosztányi Z, Paladin L, Necci M, Piovesan D (2020-07-02). "PlaToLoCo: the first web meta-server for visualization and annotation of low complexity regions in proteins". Nucleic Acids Research. 48 (W1): W77 – W84. doi:10.1093/nar/gkaa339. ISSN 0305-1048. PMC 7319588. PMID 32421769.
Ntountoumi C, Vlastaridis P, Mossialos D, Stathopoulos C, Iliopoulos I, Promponas V, Oliver SG, Amoutzias GD (2019-11-04). "Low complexity regions in the proteins of prokaryotes perform important functional roles and are highly conserved". Nucleic Acids Research. 47 (19): 9998–10009. doi:10.1093/nar/gkz730. ISSN 0305-1048. PMC 6821194. PMID 31504783.

ncbi.nlm.nih.gov

Brendel V, Bucher P, Nourbakhsh IR, Blaisdell BE, Karlin S (15 Mar 1992). "Methods and algorithms for statistical analysis of protein sequences". Proc Natl Acad Sci U S A. 89 (6): 2002–2006. Bibcode:1992PNAS...89.2002B. doi:10.1073/pnas.89.6.2002. PMC 48584. PMID 1549558.
Harrison PM (13 Nov 2017). "fLPS: Fast discovery of compositional biases for the protein universe". BMC Bioinformatics. 18 (1): 476. doi:10.1186/s12859-017-1906-3. PMC 5684748. PMID 29132292.
Ooi HS, Kwo CY, Wildpaner M, Sirota FL, Eisenhaber B, Maurer-Stroh S, Wong WC, Schleiffer A, Eisenhaber F, Schneider G (Jul 2009). "ANNIE: integrated de novo protein sequence annotation". Nucleic Acids Res. 37 (Web server issue): W435 – W440. doi:10.1093/nar/gkp254. PMC 2703921. PMID 19389726.
Harbi D, Kumar M, Harrison PM (6 Jan 2011). "LPS-annotate: complete annotation of compositionally biased regions in the protein knowledgebase". Database (Oxford). 2011: baq031. doi:10.1093/database/baq031. PMC 3017391. PMID 21216786.
Kirmitzoglou I, Promponas VJ (1 Jul 2015). "LCR-eXXXplorer: a web platform to search, visualize and share data for low complexity regions in protein sequences". Bioinformatics. 31 (13): 2208–2210. doi:10.1093/bioinformatics/btv115. PMC 4481844. PMID 25712690.
Silva JM, Qi W, Pinho AJ, Pratas D (2022-12-28). "AlcoR: alignment-free simulation, mapping, and visualization of low-complexity regions in biological data". GigaScience. 12. doi:10.1093/gigascience/giad101. ISSN 2047-217X. PMC 10716826. PMID 38091509.
Mier P, Paladin L, Tamana S, Petrosian S, Hajdu-Soltész B, Urbanek A, Gruca A, Plewczynski D, Grynberg M, Bernadó P, Gáspári Z (2020-03-23). "Disentangling the complexity of low complexity proteins". Briefings in Bioinformatics. 21 (2): 458–472. doi:10.1093/bib/bbz007. ISSN 1467-5463. PMC 7299295. PMID 30698641.
Jarnot P, Ziemska-Legiecka J, Dobson L, Merski M, Mier P, Andrade-Navarro MA, Hancock JM, Dosztányi Z, Paladin L, Necci M, Piovesan D (2020-07-02). "PlaToLoCo: the first web meta-server for visualization and annotation of low complexity regions in proteins". Nucleic Acids Research. 48 (W1): W77 – W84. doi:10.1093/nar/gkaa339. ISSN 0305-1048. PMC 7319588. PMID 32421769.
Ntountoumi C, Vlastaridis P, Mossialos D, Stathopoulos C, Iliopoulos I, Promponas V, Oliver SG, Amoutzias GD (2019-11-04). "Low complexity regions in the proteins of prokaryotes perform important functional roles and are highly conserved". Nucleic Acids Research. 47 (19): 9998–10009. doi:10.1093/nar/gkz730. ISSN 0305-1048. PMC 6821194. PMID 31504783.

semanticscholar.org

api.semanticscholar.org

Nandi T, Dash D, Ghai R, B-Rao C, Kannan K, Brahmachari SK, Ramakrishnan C, Ramachandran S (2003). "A new algorithm for detecting low-complexity regions in protein sequences". J Biomol Struct Dyn. 20 (5): 657–668. doi:10.1080/07391102.2003.10506882. PMID 12643768. S2CID 45635217.

worldcat.org

search.worldcat.org

Silva JM, Qi W, Pinho AJ, Pratas D (2022-12-28). "AlcoR: alignment-free simulation, mapping, and visualization of low-complexity regions in biological data". GigaScience. 12. doi:10.1093/gigascience/giad101. ISSN 2047-217X. PMC 10716826. PMID 38091509.
Mier P, Paladin L, Tamana S, Petrosian S, Hajdu-Soltész B, Urbanek A, Gruca A, Plewczynski D, Grynberg M, Bernadó P, Gáspári Z (2020-03-23). "Disentangling the complexity of low complexity proteins". Briefings in Bioinformatics. 21 (2): 458–472. doi:10.1093/bib/bbz007. ISSN 1467-5463. PMC 7299295. PMID 30698641.
Jarnot P, Ziemska-Legiecka J, Dobson L, Merski M, Mier P, Andrade-Navarro MA, Hancock JM, Dosztányi Z, Paladin L, Necci M, Piovesan D (2020-07-02). "PlaToLoCo: the first web meta-server for visualization and annotation of low complexity regions in proteins". Nucleic Acids Research. 48 (W1): W77 – W84. doi:10.1093/nar/gkaa339. ISSN 0305-1048. PMC 7319588. PMID 32421769.
Ntountoumi C, Vlastaridis P, Mossialos D, Stathopoulos C, Iliopoulos I, Promponas V, Oliver SG, Amoutzias GD (2019-11-04). "Low complexity regions in the proteins of prokaryotes perform important functional roles and are highly conserved". Nucleic Acids Research. 47 (19): 9998–10009. doi:10.1093/nar/gkz730. ISSN 0305-1048. PMC 6821194. PMID 31504783.