Use of mutation spectra analysis software
The study and comparison of mutation(al) spectra is an important problem in molecular biology, because these spectra often reflect on important features of mutations and their fixation. Such features include the interaction of DNA with various mutagens, the function of repair/replication enzymes, an...
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| Veröffentlicht in: | Human mutation 2001-02, Vol.17 (2), p.83-102 |
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| creator | Rogozin, Igor B. Kondrashov, Fyodor A. Glazko, Galina V. |
| description | The study and comparison of mutation(al) spectra is an important problem in molecular biology, because these spectra often reflect on important features of mutations and their fixation. Such features include the interaction of DNA with various mutagens, the function of repair/replication enzymes, and properties of target proteins. It is known that mutability varies significantly along nucleotide sequences, such that mutations often concentrate at certain positions, called “hotspots,” in a sequence. In this paper, we discuss in detail two approaches for mutation spectra analysis: the comparison of mutation spectra with a HG‐PUBL program, (FTP: sunsite.unc.edu/pub/academic/biology/dna‐mutations/hyperg) and hotspot prediction with the CLUSTERM program (www.itba.mi.cnr.it/webmutation; ftp.bionet.nsc.ru/pub/biology/dbms/clusterm.zip). Several other approaches for mutational spectra analysis, such as the analysis of a target protein structure, hotspot context revealing, multiple spectra comparisons, as well as a number of mutation databases are briefly described. Mutation spectra in the lacI gene of E. coli and the human p53 gene are used for illustration of various difficulties of such analysis. Hum Mutat 17:83–102, 2001. © 2001 Wiley‐Liss, Inc. |
| doi_str_mv | 10.1002/1098-1004(200102)17:2<83::AID-HUMU1>3.0.CO;2-E |
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Such features include the interaction of DNA with various mutagens, the function of repair/replication enzymes, and properties of target proteins. It is known that mutability varies significantly along nucleotide sequences, such that mutations often concentrate at certain positions, called “hotspots,” in a sequence. In this paper, we discuss in detail two approaches for mutation spectra analysis: the comparison of mutation spectra with a HG‐PUBL program, (FTP: sunsite.unc.edu/pub/academic/biology/dna‐mutations/hyperg) and hotspot prediction with the CLUSTERM program (www.itba.mi.cnr.it/webmutation; ftp.bionet.nsc.ru/pub/biology/dbms/clusterm.zip). Several other approaches for mutational spectra analysis, such as the analysis of a target protein structure, hotspot context revealing, multiple spectra comparisons, as well as a number of mutation databases are briefly described. Mutation spectra in the lacI gene of E. coli and the human p53 gene are used for illustration of various difficulties of such analysis. Hum Mutat 17:83–102, 2001. © 2001 Wiley‐Liss, Inc.</description><identifier>ISSN: 1059-7794</identifier><identifier>EISSN: 1098-1004</identifier><identifier>DOI: 10.1002/1098-1004(200102)17:2<83::AID-HUMU1>3.0.CO;2-E</identifier><identifier>PMID: 11180592</identifier><language>eng</language><publisher>New York: John Wiley & Sons, Inc</publisher><subject>Amino Acid Sequence ; Animals ; Base Sequence ; classification analysis ; correlation ; DNA Mutational Analysis - methods ; hotspot ; Humans ; lacI ; Molecular Sequence Data ; mutable motifs ; mutagen ; Mutation ; p53 ; phenotypic assay ; protein structure ; repair ; replication ; Sequence Homology, Amino Acid ; Sequence Homology, Nucleic Acid ; Software ; spectra comparison ; TP53 ; Tumor Suppressor Protein p53 - genetics</subject><ispartof>Human mutation, 2001-02, Vol.17 (2), p.83-102</ispartof><rights>Copyright © 2001 Wiley‐Liss, Inc.</rights><rights>Copyright 2001 Wiley-Liss, Inc.</rights><rights>Copyright © 2001 Wiley-Liss, Inc.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><cites>FETCH-LOGICAL-c4871-1f97a4bfbc3c35d7b74d34b88fd1de1e823e94775025c01ba86253e00addc263</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://onlinelibrary.wiley.com/doi/pdf/10.1002%2F1098-1004%28200102%2917%3A2%3C83%3A%3AAID-HUMU1%3E3.0.CO%3B2-E$$EPDF$$P50$$Gwiley$$H</linktopdf><linktohtml>$$Uhttps://onlinelibrary.wiley.com/doi/full/10.1002%2F1098-1004%28200102%2917%3A2%3C83%3A%3AAID-HUMU1%3E3.0.CO%3B2-E$$EHTML$$P50$$Gwiley$$H</linktohtml><link.rule.ids>314,780,784,1416,27923,27924,45573,45574</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/11180592$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Rogozin, Igor B.</creatorcontrib><creatorcontrib>Kondrashov, Fyodor A.</creatorcontrib><creatorcontrib>Glazko, Galina V.</creatorcontrib><title>Use of mutation spectra analysis software</title><title>Human mutation</title><addtitle>Hum. Mutat</addtitle><description>The study and comparison of mutation(al) spectra is an important problem in molecular biology, because these spectra often reflect on important features of mutations and their fixation. Such features include the interaction of DNA with various mutagens, the function of repair/replication enzymes, and properties of target proteins. It is known that mutability varies significantly along nucleotide sequences, such that mutations often concentrate at certain positions, called “hotspots,” in a sequence. In this paper, we discuss in detail two approaches for mutation spectra analysis: the comparison of mutation spectra with a HG‐PUBL program, (FTP: sunsite.unc.edu/pub/academic/biology/dna‐mutations/hyperg) and hotspot prediction with the CLUSTERM program (www.itba.mi.cnr.it/webmutation; ftp.bionet.nsc.ru/pub/biology/dbms/clusterm.zip). Several other approaches for mutational spectra analysis, such as the analysis of a target protein structure, hotspot context revealing, multiple spectra comparisons, as well as a number of mutation databases are briefly described. Mutation spectra in the lacI gene of E. coli and the human p53 gene are used for illustration of various difficulties of such analysis. Hum Mutat 17:83–102, 2001. © 2001 Wiley‐Liss, Inc.</description><subject>Amino Acid Sequence</subject><subject>Animals</subject><subject>Base Sequence</subject><subject>classification analysis</subject><subject>correlation</subject><subject>DNA Mutational Analysis - methods</subject><subject>hotspot</subject><subject>Humans</subject><subject>lacI</subject><subject>Molecular Sequence Data</subject><subject>mutable motifs</subject><subject>mutagen</subject><subject>Mutation</subject><subject>p53</subject><subject>phenotypic assay</subject><subject>protein structure</subject><subject>repair</subject><subject>replication</subject><subject>Sequence Homology, Amino Acid</subject><subject>Sequence Homology, Nucleic Acid</subject><subject>Software</subject><subject>spectra comparison</subject><subject>TP53</subject><subject>Tumor Suppressor Protein p53 - genetics</subject><issn>1059-7794</issn><issn>1098-1004</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2001</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><recordid>eNqNkNFO2zAUhi20abBur4AirsZFunPsJHY6hIS6DtBYW4mWcnfkJI4UaJtipyp9e9ylKje72JV_Hf_-jvUxliB0EYB_R0hV6FP0jQMg8HOUPX6hRK93dfszvJn-meKl6EK3P_rBw8EROzk8-LDLcRpKmUbH7LNzTwCg4lh8YseIqPwdP2HnU2eCugwW60Y3Vb0M3MrkjdWBXur51lUucHXZbLQ1X9jHUs-d-bo_O2zyazDp34R3o-vb_tVdmEdKYohlKnWUlVkuchEXMpNRIaJMqbLAwqBRXJg0kjIGHueAmVYJj4UB0EWR80R02FmLXdn6ZW1cQ0_12vrPOMJU8kRxnvrSsC3ltnbOmpJWtlpouyUE2nmjnYZdiqj1RiiJkxJE3hv99UaCgPojPx544Ol-6zpbmOIdtxflC-O2sKnmZvv_6_61rR14ZNgiK9eY1wNS22dKpJAxzYbXNJvwh_H970eaiDe4CJMX</recordid><startdate>200102</startdate><enddate>200102</enddate><creator>Rogozin, Igor B.</creator><creator>Kondrashov, Fyodor A.</creator><creator>Glazko, Galina V.</creator><general>John Wiley & Sons, Inc</general><general>Hindawi Limited</general><scope>BSCLL</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>3V.</scope><scope>7QP</scope><scope>7TK</scope><scope>7X7</scope><scope>7XB</scope><scope>88A</scope><scope>88E</scope><scope>8C1</scope><scope>8FD</scope><scope>8FE</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BHPHI</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>LK8</scope><scope>M0S</scope><scope>M1P</scope><scope>M7P</scope><scope>P64</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>RC3</scope></search><sort><creationdate>200102</creationdate><title>Use of mutation spectra analysis software</title><author>Rogozin, Igor B. ; Kondrashov, Fyodor A. ; Glazko, Galina V.</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c4871-1f97a4bfbc3c35d7b74d34b88fd1de1e823e94775025c01ba86253e00addc263</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2001</creationdate><topic>Amino Acid Sequence</topic><topic>Animals</topic><topic>Base Sequence</topic><topic>classification analysis</topic><topic>correlation</topic><topic>DNA Mutational Analysis - methods</topic><topic>hotspot</topic><topic>Humans</topic><topic>lacI</topic><topic>Molecular Sequence Data</topic><topic>mutable motifs</topic><topic>mutagen</topic><topic>Mutation</topic><topic>p53</topic><topic>phenotypic assay</topic><topic>protein structure</topic><topic>repair</topic><topic>replication</topic><topic>Sequence Homology, Amino Acid</topic><topic>Sequence Homology, Nucleic Acid</topic><topic>Software</topic><topic>spectra comparison</topic><topic>TP53</topic><topic>Tumor Suppressor Protein p53 - genetics</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Rogozin, Igor B.</creatorcontrib><creatorcontrib>Kondrashov, Fyodor A.</creatorcontrib><creatorcontrib>Glazko, Galina V.</creatorcontrib><collection>Istex</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>ProQuest Central (Corporate)</collection><collection>Calcium & Calcified Tissue Abstracts</collection><collection>Neurosciences Abstracts</collection><collection>Health & Medical Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Biology Database (Alumni Edition)</collection><collection>Medical Database (Alumni Edition)</collection><collection>Public Health Database</collection><collection>Technology Research Database</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>Hospital Premium Collection</collection><collection>Hospital Premium Collection (Alumni Edition)</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>ProQuest Central (Alumni Edition)</collection><collection>ProQuest Central UK/Ireland</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>Natural Science Collection</collection><collection>ProQuest One Community College</collection><collection>ProQuest Central Korea</collection><collection>Engineering Research Database</collection><collection>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>ProQuest Central Student</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>ProQuest Biological Science Collection</collection><collection>Health & Medical Collection (Alumni Edition)</collection><collection>Medical Database</collection><collection>Biological Science Database</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Publicly Available Content Database</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>ProQuest Central China</collection><collection>Genetics Abstracts</collection><jtitle>Human mutation</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Rogozin, Igor B.</au><au>Kondrashov, Fyodor A.</au><au>Glazko, Galina V.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Use of mutation spectra analysis software</atitle><jtitle>Human mutation</jtitle><addtitle>Hum. Mutat</addtitle><date>2001-02</date><risdate>2001</risdate><volume>17</volume><issue>2</issue><spage>83</spage><epage>102</epage><pages>83-102</pages><issn>1059-7794</issn><eissn>1098-1004</eissn><abstract>The study and comparison of mutation(al) spectra is an important problem in molecular biology, because these spectra often reflect on important features of mutations and their fixation. Such features include the interaction of DNA with various mutagens, the function of repair/replication enzymes, and properties of target proteins. It is known that mutability varies significantly along nucleotide sequences, such that mutations often concentrate at certain positions, called “hotspots,” in a sequence. In this paper, we discuss in detail two approaches for mutation spectra analysis: the comparison of mutation spectra with a HG‐PUBL program, (FTP: sunsite.unc.edu/pub/academic/biology/dna‐mutations/hyperg) and hotspot prediction with the CLUSTERM program (www.itba.mi.cnr.it/webmutation; ftp.bionet.nsc.ru/pub/biology/dbms/clusterm.zip). Several other approaches for mutational spectra analysis, such as the analysis of a target protein structure, hotspot context revealing, multiple spectra comparisons, as well as a number of mutation databases are briefly described. Mutation spectra in the lacI gene of E. coli and the human p53 gene are used for illustration of various difficulties of such analysis. Hum Mutat 17:83–102, 2001. © 2001 Wiley‐Liss, Inc.</abstract><cop>New York</cop><pub>John Wiley & Sons, Inc</pub><pmid>11180592</pmid><doi>10.1002/1098-1004(200102)17:2<83::AID-HUMU1>3.0.CO;2-E</doi><tpages>20</tpages><oa>free_for_read</oa></addata></record> |
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| subjects | Amino Acid Sequence Animals Base Sequence classification analysis correlation DNA Mutational Analysis - methods hotspot Humans lacI Molecular Sequence Data mutable motifs mutagen Mutation p53 phenotypic assay protein structure repair replication Sequence Homology, Amino Acid Sequence Homology, Nucleic Acid Software spectra comparison TP53 Tumor Suppressor Protein p53 - genetics |
| title | Use of mutation spectra analysis software |
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