Profile analysis: detection of distantly related proteins
Profile analysis is a method for detecting distantly related proteins by sequence comparison. The basis for comparison is not only the customary Dayhoff mutational-distance matrix but also the results of structural studies and information implicit in the alignments of the sequences of families of si...
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| Veröffentlicht in: | Proceedings of the National Academy of Sciences - PNAS 1987-07, Vol.84 (13), p.4355-4358 |
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| container_title | Proceedings of the National Academy of Sciences - PNAS |
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| creator | Gribskov, M McLachlan, A.D Eisenberg, D |
| description | Profile analysis is a method for detecting distantly related proteins by sequence comparison. The basis for comparison is not only the customary Dayhoff mutational-distance matrix but also the results of structural studies and information implicit in the alignments of the sequences of families of similar proteins. This information is expressed in a position-specific scoring table (profile), which is created from a group of sequences previously aligned by structural or sequence similarity. The similarity of any other sequence (target) to the group of aligned sequences (probe) can be tested by comparing the target to the profile using dynamic programming algorithms. The profile method differs in two major respects from methods of sequence comparison in common use: (i) Any number of known sequences can be used to construct the profile, allowing more information to be used in the testing of the target than is possible with pairwise alignment methods. (ii) The profile includes the penalties for insertion or deletion at each position, which allow one to include the probe secondary structure in the testing scheme. Tests with globin and immunoglobulin sequences show that profile analysis can distinguish all members of these families from all other sequences in a database containing 3800 protein sequences. |
| doi_str_mv | 10.1073/pnas.84.13.4355 |
| format | Article |
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The basis for comparison is not only the customary Dayhoff mutational-distance matrix but also the results of structural studies and information implicit in the alignments of the sequences of families of similar proteins. This information is expressed in a position-specific scoring table (profile), which is created from a group of sequences previously aligned by structural or sequence similarity. The similarity of any other sequence (target) to the group of aligned sequences (probe) can be tested by comparing the target to the profile using dynamic programming algorithms. The profile method differs in two major respects from methods of sequence comparison in common use: (i) Any number of known sequences can be used to construct the profile, allowing more information to be used in the testing of the target than is possible with pairwise alignment methods. (ii) The profile includes the penalties for insertion or deletion at each position, which allow one to include the probe secondary structure in the testing scheme. Tests with globin and immunoglobulin sequences show that profile analysis can distinguish all members of these families from all other sequences in a database containing 3800 protein sequences.</description><identifier>ISSN: 0027-8424</identifier><identifier>EISSN: 1091-6490</identifier><identifier>DOI: 10.1073/pnas.84.13.4355</identifier><identifier>PMID: 3474607</identifier><identifier>CODEN: PNASA6</identifier><language>eng</language><publisher>Washington, DC: National Academy of Sciences of the United States of America</publisher><subject>ACIDE AMINE ; Algorithms ; Amino Acid Sequence ; AMINO ACIDS ; AMINOACIDOS ; Analytical, structural and metabolic biochemistry ; ANIMAL PROTEIN ; Base Sequence ; Biochemistry ; Biological and medical sciences ; COMPUTER SOFTWARE ; Dynamic programming methods ; Fundamental and applied biological sciences. Psychology ; General aspects, investigation methods ; GLOBINS ; Globins - genetics ; Immunoglobulin constant regions ; IMMUNOGLOBULINE ; IMMUNOGLOBULINS ; Immunoglobulins - genetics ; Information search ; Information Systems ; INMUNOGLOBULINA ; LOGICIEL ; Molecular structure ; Nucleic acids ; PLANT PROTEINS ; PROFMAKE PROGRAM ; PROGRAMAS DE ORDENADOR ; Protein Conformation ; PROTEINAS DE ORIGEN ANIMAL ; PROTEINAS VEGETALES ; PROTEINE ANIMALE ; PROTEINE VEGETALE ; Proteins ; Proteins - genetics ; Sequence Homology, Nucleic Acid ; Software</subject><ispartof>Proceedings of the National Academy of Sciences - PNAS, 1987-07, Vol.84 (13), p.4355-4358</ispartof><rights>1987 INIST-CNRS</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c577t-3a1793ddeff8d5c0b1f17845d757182a91bd6e4341f8ab4ead507e5c83b0d8443</citedby></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Uhttp://www.pnas.org/content/84/13.cover.gif</thumbnail><linktopdf>$$Uhttps://www.jstor.org/stable/pdf/30172$$EPDF$$P50$$Gjstor$$H</linktopdf><linktohtml>$$Uhttps://www.jstor.org/stable/30172$$EHTML$$P50$$Gjstor$$H</linktohtml><link.rule.ids>230,314,723,776,780,799,881,27901,27902,53766,53768,57992,58225</link.rule.ids><backlink>$$Uhttp://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=8321878$$DView record in Pascal Francis$$Hfree_for_read</backlink><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/3474607$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Gribskov, M</creatorcontrib><creatorcontrib>McLachlan, A.D</creatorcontrib><creatorcontrib>Eisenberg, D</creatorcontrib><title>Profile analysis: detection of distantly related proteins</title><title>Proceedings of the National Academy of Sciences - PNAS</title><addtitle>Proc Natl Acad Sci U S A</addtitle><description>Profile analysis is a method for detecting distantly related proteins by sequence comparison. The basis for comparison is not only the customary Dayhoff mutational-distance matrix but also the results of structural studies and information implicit in the alignments of the sequences of families of similar proteins. This information is expressed in a position-specific scoring table (profile), which is created from a group of sequences previously aligned by structural or sequence similarity. The similarity of any other sequence (target) to the group of aligned sequences (probe) can be tested by comparing the target to the profile using dynamic programming algorithms. The profile method differs in two major respects from methods of sequence comparison in common use: (i) Any number of known sequences can be used to construct the profile, allowing more information to be used in the testing of the target than is possible with pairwise alignment methods. (ii) The profile includes the penalties for insertion or deletion at each position, which allow one to include the probe secondary structure in the testing scheme. Tests with globin and immunoglobulin sequences show that profile analysis can distinguish all members of these families from all other sequences in a database containing 3800 protein sequences.</description><subject>ACIDE AMINE</subject><subject>Algorithms</subject><subject>Amino Acid Sequence</subject><subject>AMINO ACIDS</subject><subject>AMINOACIDOS</subject><subject>Analytical, structural and metabolic biochemistry</subject><subject>ANIMAL PROTEIN</subject><subject>Base Sequence</subject><subject>Biochemistry</subject><subject>Biological and medical sciences</subject><subject>COMPUTER SOFTWARE</subject><subject>Dynamic programming methods</subject><subject>Fundamental and applied biological sciences. Psychology</subject><subject>General aspects, investigation methods</subject><subject>GLOBINS</subject><subject>Globins - genetics</subject><subject>Immunoglobulin constant regions</subject><subject>IMMUNOGLOBULINE</subject><subject>IMMUNOGLOBULINS</subject><subject>Immunoglobulins - genetics</subject><subject>Information search</subject><subject>Information Systems</subject><subject>INMUNOGLOBULINA</subject><subject>LOGICIEL</subject><subject>Molecular structure</subject><subject>Nucleic acids</subject><subject>PLANT PROTEINS</subject><subject>PROFMAKE PROGRAM</subject><subject>PROGRAMAS DE ORDENADOR</subject><subject>Protein Conformation</subject><subject>PROTEINAS DE ORIGEN ANIMAL</subject><subject>PROTEINAS VEGETALES</subject><subject>PROTEINE ANIMALE</subject><subject>PROTEINE VEGETALE</subject><subject>Proteins</subject><subject>Proteins - genetics</subject><subject>Sequence Homology, Nucleic Acid</subject><subject>Software</subject><issn>0027-8424</issn><issn>1091-6490</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>1987</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNp9kMFrFDEUh4Moda2eBVGZg-hpti-TZJIRPEixrVBQ0J7Dm0lSU7KTNckW9793lh1GvXh6h-_7vff4EfKcwpqCZGfbEfNa8TVla86EeEBWFDpat7yDh2QF0Mha8YY_Jk9yvgOATig4ISeMS96CXJHua4rOB1vhiGGffX5fGVvsUHwcq-gq43PBsYR9lWzAYk21TbFYP-an5JHDkO2zeZ6Sm4tP38-v6usvl5_PP17Xg5Cy1Ayp7Jgx1jllxAA9dVQqLowUkqoGO9qb1nLGqVPYc4tGgLRiUKwHozhnp-TDce9212-sGexYEga9TX6Daa8jev0vGf0PfRvvNQMBSk75t3M-xZ87m4ve-DzYEHC0cZe1lC1QrtpJPDuKQ4o5J-uWGxT0oWx9KFsrrinTh7KnxKu_X1v8ud2Jv5k55gGDSzgOPi-aYg1VUk3au1k77F_ocke7XQjF_iqT-fq_5iS8OAp3ucT05yGgspngyyN0GDXepumVm29KctkqqhT7DV0Nsoc</recordid><startdate>19870701</startdate><enddate>19870701</enddate><creator>Gribskov, M</creator><creator>McLachlan, A.D</creator><creator>Eisenberg, D</creator><general>National Academy of Sciences of the United States of America</general><general>National Acad Sciences</general><scope>FBQ</scope><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>7X8</scope><scope>5PM</scope></search><sort><creationdate>19870701</creationdate><title>Profile analysis: detection of distantly related proteins</title><author>Gribskov, M ; McLachlan, A.D ; Eisenberg, D</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c577t-3a1793ddeff8d5c0b1f17845d757182a91bd6e4341f8ab4ead507e5c83b0d8443</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>1987</creationdate><topic>ACIDE AMINE</topic><topic>Algorithms</topic><topic>Amino Acid Sequence</topic><topic>AMINO ACIDS</topic><topic>AMINOACIDOS</topic><topic>Analytical, structural and metabolic biochemistry</topic><topic>ANIMAL PROTEIN</topic><topic>Base Sequence</topic><topic>Biochemistry</topic><topic>Biological and medical sciences</topic><topic>COMPUTER SOFTWARE</topic><topic>Dynamic programming methods</topic><topic>Fundamental and applied biological sciences. Psychology</topic><topic>General aspects, investigation methods</topic><topic>GLOBINS</topic><topic>Globins - genetics</topic><topic>Immunoglobulin constant regions</topic><topic>IMMUNOGLOBULINE</topic><topic>IMMUNOGLOBULINS</topic><topic>Immunoglobulins - genetics</topic><topic>Information search</topic><topic>Information Systems</topic><topic>INMUNOGLOBULINA</topic><topic>LOGICIEL</topic><topic>Molecular structure</topic><topic>Nucleic acids</topic><topic>PLANT PROTEINS</topic><topic>PROFMAKE PROGRAM</topic><topic>PROGRAMAS DE ORDENADOR</topic><topic>Protein Conformation</topic><topic>PROTEINAS DE ORIGEN ANIMAL</topic><topic>PROTEINAS VEGETALES</topic><topic>PROTEINE ANIMALE</topic><topic>PROTEINE VEGETALE</topic><topic>Proteins</topic><topic>Proteins - genetics</topic><topic>Sequence Homology, Nucleic Acid</topic><topic>Software</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Gribskov, M</creatorcontrib><creatorcontrib>McLachlan, A.D</creatorcontrib><creatorcontrib>Eisenberg, D</creatorcontrib><collection>AGRIS</collection><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>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Proceedings of the National Academy of Sciences - PNAS</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Gribskov, M</au><au>McLachlan, A.D</au><au>Eisenberg, D</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Profile analysis: detection of distantly related proteins</atitle><jtitle>Proceedings of the National Academy of Sciences - PNAS</jtitle><addtitle>Proc Natl Acad Sci U S A</addtitle><date>1987-07-01</date><risdate>1987</risdate><volume>84</volume><issue>13</issue><spage>4355</spage><epage>4358</epage><pages>4355-4358</pages><issn>0027-8424</issn><eissn>1091-6490</eissn><coden>PNASA6</coden><abstract>Profile analysis is a method for detecting distantly related proteins by sequence comparison. The basis for comparison is not only the customary Dayhoff mutational-distance matrix but also the results of structural studies and information implicit in the alignments of the sequences of families of similar proteins. This information is expressed in a position-specific scoring table (profile), which is created from a group of sequences previously aligned by structural or sequence similarity. The similarity of any other sequence (target) to the group of aligned sequences (probe) can be tested by comparing the target to the profile using dynamic programming algorithms. The profile method differs in two major respects from methods of sequence comparison in common use: (i) Any number of known sequences can be used to construct the profile, allowing more information to be used in the testing of the target than is possible with pairwise alignment methods. (ii) The profile includes the penalties for insertion or deletion at each position, which allow one to include the probe secondary structure in the testing scheme. Tests with globin and immunoglobulin sequences show that profile analysis can distinguish all members of these families from all other sequences in a database containing 3800 protein sequences.</abstract><cop>Washington, DC</cop><pub>National Academy of Sciences of the United States of America</pub><pmid>3474607</pmid><doi>10.1073/pnas.84.13.4355</doi><tpages>4</tpages><oa>free_for_read</oa></addata></record> |
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| ispartof | Proceedings of the National Academy of Sciences - PNAS, 1987-07, Vol.84 (13), p.4355-4358 |
| issn | 0027-8424 1091-6490 |
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| source | Jstor Complete Legacy; MEDLINE; PubMed Central; Alma/SFX Local Collection; Free Full-Text Journals in Chemistry |
| subjects | ACIDE AMINE Algorithms Amino Acid Sequence AMINO ACIDS AMINOACIDOS Analytical, structural and metabolic biochemistry ANIMAL PROTEIN Base Sequence Biochemistry Biological and medical sciences COMPUTER SOFTWARE Dynamic programming methods Fundamental and applied biological sciences. Psychology General aspects, investigation methods GLOBINS Globins - genetics Immunoglobulin constant regions IMMUNOGLOBULINE IMMUNOGLOBULINS Immunoglobulins - genetics Information search Information Systems INMUNOGLOBULINA LOGICIEL Molecular structure Nucleic acids PLANT PROTEINS PROFMAKE PROGRAM PROGRAMAS DE ORDENADOR Protein Conformation PROTEINAS DE ORIGEN ANIMAL PROTEINAS VEGETALES PROTEINE ANIMALE PROTEINE VEGETALE Proteins Proteins - genetics Sequence Homology, Nucleic Acid Software |
| title | Profile analysis: detection of distantly related proteins |
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