Loading…
Temperature Influences Synonymous Codon and Amino Acid Usage Biases in the Phages Infecting Extremely Thermophilic Prokaryotes
To see the effect of temperature on the codon and amino acid usage in phages, codon and amino acid usage of 13 phages of extremely thermophilic prokaryotes were compared with that of 14 phages of mesophilic prokaryotes. Correspondence analysis on RSCU values of two groups of phage genomes clearly sh...
Saved in:
| Published in: | In silico biology 2009, Vol.9 (1-2), p.1-9 |
|---|---|
| Main Authors: | , |
| Format: | Article |
| Language: | English |
| Subjects: | |
| Citations: | Items that cite this one |
| Online Access: | Get full text |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| cited_by | cdi_FETCH-LOGICAL-c302t-64ef2dd830c3a11c69ca9362c0ededa736027cea7ac0c7d330df7285ffe80ecd3 |
|---|---|
| cites | |
| container_end_page | 9 |
| container_issue | 1-2 |
| container_start_page | 1 |
| container_title | In silico biology |
| container_volume | 9 |
| creator | Sau, Keya Deb, Arpan |
| description | To see the effect of temperature on the codon and amino acid usage
in phages, codon and amino acid usage of 13 phages of extremely thermophilic
prokaryotes were compared with that of 14 phages of mesophilic prokaryotes.
Correspondence analysis on RSCU values of two groups of phage genomes clearly
shows that phages are separated along the second major axis according to their
growth temperature, whereas, they are separated along the first major axis
according to their GC content. Correspondence analysis on RAAU values of two
groups of phages clearly shows that protein encoding genes of the phages along
the second major axis are highly correlated with the GRAVY, aromaticity and
cysteine content. Moreover, correspondence analysis on the regular and
irregular structures of proteins of phages infecting extremely thermophilic
prokaryotes reveals that temperature is one of the factors responsible for most
significant differentiation of codon and amino acid usages variation in these
phages. |
| doi_str_mv | 10.3233/ISB-2009-0383 |
| format | article |
| fullrecord | <record><control><sourceid>proquest_cross</sourceid><recordid>TN_cdi_proquest_miscellaneous_67393125</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><sage_id>10.3233_ISB-2009-0383</sage_id><sourcerecordid>67393125</sourcerecordid><originalsourceid>FETCH-LOGICAL-c302t-64ef2dd830c3a11c69ca9362c0ededa736027cea7ac0c7d330df7285ffe80ecd3</originalsourceid><addsrcrecordid>eNqF0c-L1DAUB_AgivtDj14lFz0sVF_y2qY9zg6rDiy4sLPnEpPXnaxtMiYtOBf_dlNm0JN4SggfvsnLl7E3Aj6gRPy4ub8uJEBbADb4jJ2LEssCJajneY9NXdSIzRm7SOkJAJpSli_ZmWgrVKJS5-zXlsY9RT3NkfjG98NM3lDi9wcf_GEMc-LrYIPn2lu-Gp0PfGWc5Q9JPxK_djpl7DyfdsTvdvksLSlkJucf-c3PKdJIw4FvdxTHsN-5wRl-F8N3HQ9hovSKvej1kOj1ab1kD59utusvxe3Xz5v16rYwCHIq6pJ6aW2DYFALYerW6BZraYAsWa2wBqkMaaUNGGURwfZKNlXfUwNkLF6y98fcfQw_ZkpTN7pkaBi0pzxjVytsUcjqv1BCWaqybjMsjtDEkFKkvttHN-axOgHd0kyXm-mWZrqlmezfnoLnbyPZv_pURQbvTkAno4c-am9c-uNkfl0Dlcju6uiWBrqnMEeff-4ft_4GChulNQ</addsrcrecordid><sourcetype>Aggregation Database</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>20447469</pqid></control><display><type>article</type><title>Temperature Influences Synonymous Codon and Amino Acid Usage Biases in the Phages Infecting Extremely Thermophilic Prokaryotes</title><source>Full-Text Journals in Chemistry (Open access)</source><creator>Sau, Keya ; Deb, Arpan</creator><creatorcontrib>Sau, Keya ; Deb, Arpan</creatorcontrib><description>To see the effect of temperature on the codon and amino acid usage
in phages, codon and amino acid usage of 13 phages of extremely thermophilic
prokaryotes were compared with that of 14 phages of mesophilic prokaryotes.
Correspondence analysis on RSCU values of two groups of phage genomes clearly
shows that phages are separated along the second major axis according to their
growth temperature, whereas, they are separated along the first major axis
according to their GC content. Correspondence analysis on RAAU values of two
groups of phages clearly shows that protein encoding genes of the phages along
the second major axis are highly correlated with the GRAVY, aromaticity and
cysteine content. Moreover, correspondence analysis on the regular and
irregular structures of proteins of phages infecting extremely thermophilic
prokaryotes reveals that temperature is one of the factors responsible for most
significant differentiation of codon and amino acid usages variation in these
phages.</description><identifier>ISSN: 1386-6338</identifier><identifier>EISSN: 1434-3207</identifier><identifier>DOI: 10.3233/ISB-2009-0383</identifier><identifier>PMID: 19537157</identifier><language>eng</language><publisher>London, England: SAGE Publications</publisher><subject>Amino Acids - analysis ; Archaea - genetics ; Archaea - growth & development ; Bacteriophages - genetics ; Bacteriophages - pathogenicity ; Base Composition ; Biological and medical sciences ; Codon - genetics ; Fundamental and applied biological sciences. Psychology ; General aspects ; Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects) ; Prokaryotic Cells - microbiology ; Temperature</subject><ispartof>In silico biology, 2009, Vol.9 (1-2), p.1-9</ispartof><rights>IOS Press. All rights reserved</rights><rights>2009 INIST-CNRS</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c302t-64ef2dd830c3a11c69ca9362c0ededa736027cea7ac0c7d330df7285ffe80ecd3</citedby></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>314,777,781,4010,27904,27905,27906</link.rule.ids><backlink>$$Uhttp://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=21258051$$DView record in Pascal Francis$$Hfree_for_read</backlink><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/19537157$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Sau, Keya</creatorcontrib><creatorcontrib>Deb, Arpan</creatorcontrib><title>Temperature Influences Synonymous Codon and Amino Acid Usage Biases in the Phages Infecting Extremely Thermophilic Prokaryotes</title><title>In silico biology</title><addtitle>In Silico Biol</addtitle><description>To see the effect of temperature on the codon and amino acid usage
in phages, codon and amino acid usage of 13 phages of extremely thermophilic
prokaryotes were compared with that of 14 phages of mesophilic prokaryotes.
Correspondence analysis on RSCU values of two groups of phage genomes clearly
shows that phages are separated along the second major axis according to their
growth temperature, whereas, they are separated along the first major axis
according to their GC content. Correspondence analysis on RAAU values of two
groups of phages clearly shows that protein encoding genes of the phages along
the second major axis are highly correlated with the GRAVY, aromaticity and
cysteine content. Moreover, correspondence analysis on the regular and
irregular structures of proteins of phages infecting extremely thermophilic
prokaryotes reveals that temperature is one of the factors responsible for most
significant differentiation of codon and amino acid usages variation in these
phages.</description><subject>Amino Acids - analysis</subject><subject>Archaea - genetics</subject><subject>Archaea - growth & development</subject><subject>Bacteriophages - genetics</subject><subject>Bacteriophages - pathogenicity</subject><subject>Base Composition</subject><subject>Biological and medical sciences</subject><subject>Codon - genetics</subject><subject>Fundamental and applied biological sciences. Psychology</subject><subject>General aspects</subject><subject>Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects)</subject><subject>Prokaryotic Cells - microbiology</subject><subject>Temperature</subject><issn>1386-6338</issn><issn>1434-3207</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2009</creationdate><recordtype>article</recordtype><recordid>eNqF0c-L1DAUB_AgivtDj14lFz0sVF_y2qY9zg6rDiy4sLPnEpPXnaxtMiYtOBf_dlNm0JN4SggfvsnLl7E3Aj6gRPy4ub8uJEBbADb4jJ2LEssCJajneY9NXdSIzRm7SOkJAJpSli_ZmWgrVKJS5-zXlsY9RT3NkfjG98NM3lDi9wcf_GEMc-LrYIPn2lu-Gp0PfGWc5Q9JPxK_djpl7DyfdsTvdvksLSlkJucf-c3PKdJIw4FvdxTHsN-5wRl-F8N3HQ9hovSKvej1kOj1ab1kD59utusvxe3Xz5v16rYwCHIq6pJ6aW2DYFALYerW6BZraYAsWa2wBqkMaaUNGGURwfZKNlXfUwNkLF6y98fcfQw_ZkpTN7pkaBi0pzxjVytsUcjqv1BCWaqybjMsjtDEkFKkvttHN-axOgHd0kyXm-mWZrqlmezfnoLnbyPZv_pURQbvTkAno4c-am9c-uNkfl0Dlcju6uiWBrqnMEeff-4ft_4GChulNQ</recordid><startdate>2009</startdate><enddate>2009</enddate><creator>Sau, Keya</creator><creator>Deb, Arpan</creator><general>SAGE Publications</general><general>IOS Press</general><scope>IQODW</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7QO</scope><scope>7TM</scope><scope>8FD</scope><scope>FR3</scope><scope>P64</scope><scope>RC3</scope><scope>7X8</scope></search><sort><creationdate>2009</creationdate><title>Temperature Influences Synonymous Codon and Amino Acid Usage Biases in the Phages Infecting Extremely Thermophilic Prokaryotes</title><author>Sau, Keya ; Deb, Arpan</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c302t-64ef2dd830c3a11c69ca9362c0ededa736027cea7ac0c7d330df7285ffe80ecd3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2009</creationdate><topic>Amino Acids - analysis</topic><topic>Archaea - genetics</topic><topic>Archaea - growth & development</topic><topic>Bacteriophages - genetics</topic><topic>Bacteriophages - pathogenicity</topic><topic>Base Composition</topic><topic>Biological and medical sciences</topic><topic>Codon - genetics</topic><topic>Fundamental and applied biological sciences. Psychology</topic><topic>General aspects</topic><topic>Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects)</topic><topic>Prokaryotic Cells - microbiology</topic><topic>Temperature</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Sau, Keya</creatorcontrib><creatorcontrib>Deb, Arpan</creatorcontrib><collection>Pascal-Francis</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Biotechnology Research Abstracts</collection><collection>Nucleic Acids Abstracts</collection><collection>Technology Research Database</collection><collection>Engineering Research Database</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><jtitle>In silico biology</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Sau, Keya</au><au>Deb, Arpan</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Temperature Influences Synonymous Codon and Amino Acid Usage Biases in the Phages Infecting Extremely Thermophilic Prokaryotes</atitle><jtitle>In silico biology</jtitle><addtitle>In Silico Biol</addtitle><date>2009</date><risdate>2009</risdate><volume>9</volume><issue>1-2</issue><spage>1</spage><epage>9</epage><pages>1-9</pages><issn>1386-6338</issn><eissn>1434-3207</eissn><abstract>To see the effect of temperature on the codon and amino acid usage
in phages, codon and amino acid usage of 13 phages of extremely thermophilic
prokaryotes were compared with that of 14 phages of mesophilic prokaryotes.
Correspondence analysis on RSCU values of two groups of phage genomes clearly
shows that phages are separated along the second major axis according to their
growth temperature, whereas, they are separated along the first major axis
according to their GC content. Correspondence analysis on RAAU values of two
groups of phages clearly shows that protein encoding genes of the phages along
the second major axis are highly correlated with the GRAVY, aromaticity and
cysteine content. Moreover, correspondence analysis on the regular and
irregular structures of proteins of phages infecting extremely thermophilic
prokaryotes reveals that temperature is one of the factors responsible for most
significant differentiation of codon and amino acid usages variation in these
phages.</abstract><cop>London, England</cop><pub>SAGE Publications</pub><pmid>19537157</pmid><doi>10.3233/ISB-2009-0383</doi><tpages>9</tpages></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 1386-6338 |
| ispartof | In silico biology, 2009, Vol.9 (1-2), p.1-9 |
| issn | 1386-6338 1434-3207 |
| language | eng |
| recordid | cdi_proquest_miscellaneous_67393125 |
| source | Full-Text Journals in Chemistry (Open access) |
| subjects | Amino Acids - analysis Archaea - genetics Archaea - growth & development Bacteriophages - genetics Bacteriophages - pathogenicity Base Composition Biological and medical sciences Codon - genetics Fundamental and applied biological sciences. Psychology General aspects Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects) Prokaryotic Cells - microbiology Temperature |
| title | Temperature Influences Synonymous Codon and Amino Acid Usage Biases in the Phages Infecting Extremely Thermophilic Prokaryotes |
| url | http://sfxeu10.hosted.exlibrisgroup.com/loughborough?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-01-20T07%3A48%3A46IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-proquest_cross&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Temperature%20Influences%20Synonymous%20Codon%20and%20Amino%20Acid%20Usage%20Biases%20in%20the%20Phages%20Infecting%20Extremely%20Thermophilic%20Prokaryotes&rft.jtitle=In%20silico%20biology&rft.au=Sau,%20Keya&rft.date=2009&rft.volume=9&rft.issue=1-2&rft.spage=1&rft.epage=9&rft.pages=1-9&rft.issn=1386-6338&rft.eissn=1434-3207&rft_id=info:doi/10.3233/ISB-2009-0383&rft_dat=%3Cproquest_cross%3E67393125%3C/proquest_cross%3E%3Cgrp_id%3Ecdi_FETCH-LOGICAL-c302t-64ef2dd830c3a11c69ca9362c0ededa736027cea7ac0c7d330df7285ffe80ecd3%3C/grp_id%3E%3Coa%3E%3C/oa%3E%3Curl%3E%3C/url%3E&rft_id=info:oai/&rft_pqid=20447469&rft_id=info:pmid/19537157&rft_sage_id=10.3233_ISB-2009-0383&rfr_iscdi=true |