Friend, an integrated analytical front-end application for bioinformatics.
Identifieur interne : 000175 ( PubMed/Curation ); précédent : 000174; suivant : 000176Friend, an integrated analytical front-end application for bioinformatics.
Auteurs : Alexej Abyzov [États-Unis] ; Mounir Errami ; Chesley M. Leslin ; Valentin A. IlyinSource :
- Bioinformatics (Oxford, England) [ 1367-4803 ] ; 2005.
English descriptors
- KwdEn :
- Computational Biology (instrumentation), Computational Biology (methods), Computer Graphics, DNA (chemistry), Database Management Systems, Databases, Genetic, Databases, Protein, Exons, Internet, Muramidase (chemistry), Nucleic Acid Conformation, Phylogeny, Protein Folding, Proteins, RNA (chemistry), Sequence Alignment, Sequence Analysis, Protein, Software, User-Computer Interface.
- MESH :
- chemical , chemistry : DNA, Muramidase, RNA.
- instrumentation : Computational Biology.
- methods : Computational Biology.
- Computer Graphics, Database Management Systems, Databases, Genetic, Databases, Protein, Exons, Internet, Nucleic Acid Conformation, Phylogeny, Protein Folding, Proteins, Sequence Alignment, Sequence Analysis, Protein, Software, User-Computer Interface.
Abstract
Friend is a bioinformatics application designed for simultaneous analysis and visualization of multiple structures and sequences of proteins and/or DNA/RNA. The application provides basic functionalities, such as structure visualization, with different rendering and coloring, sequence alignment and simple phylogeny analysis, along with a number of extended features to perform more complex analyses of sequence structure relationships, including structural alignment of proteins, investigation of specific interaction motifs, studies of protein-protein and protein-DNA interactions and protein super-families. It is also useful for functional annotation of proteins, protein modeling and protein folding studies. Friend provides three levels of usage: (1) an extensive GUI for a scientist with no programming experience, (2) a command line interface for scripting for a scientist with some programming experience and (3) the ability to extend Friend with user written libraries for an experienced programmer. The application is linked and communicates with local and remote sequence and structure databases.
DOI: 10.1093/bioinformatics/bti602
PubMed: 16076889
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Ilyin</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2005">2005</date><idno type="doi">10.1093/bioinformatics/bti602</idno><idno type="RBID">pubmed:16076889</idno><idno type="pmid">16076889</idno><idno type="wicri:Area/PubMed/Corpus">000175</idno><idno type="wicri:Area/PubMed/Curation">000175</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Friend, an integrated analytical front-end application for bioinformatics.</title><author><name sortKey="Abyzov, Alexej" sort="Abyzov, Alexej" uniqKey="Abyzov A" first="Alexej" last="Abyzov">Alexej Abyzov</name><affiliation wicri:level="1"><nlm:affiliation>Department of Biology, Northeastern University, Boston, MA, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Biology, Northeastern University, Boston, MA</wicri:regionArea></affiliation></author><author><name sortKey="Errami, Mounir" sort="Errami, Mounir" uniqKey="Errami M" first="Mounir" last="Errami">Mounir Errami</name></author><author><name sortKey="Leslin, Chesley M" sort="Leslin, Chesley M" uniqKey="Leslin C" first="Chesley M" last="Leslin">Chesley M. Leslin</name></author><author><name sortKey="Ilyin, Valentin A" sort="Ilyin, Valentin A" uniqKey="Ilyin V" first="Valentin A" last="Ilyin">Valentin A. Ilyin</name></author></analytic><series><title level="j">Bioinformatics (Oxford, England)</title><idno type="ISSN">1367-4803</idno><imprint><date when="2005" type="published">2005</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Computational Biology (instrumentation)</term><term>Computational Biology (methods)</term><term>Computer Graphics</term><term>DNA (chemistry)</term><term>Database Management Systems</term><term>Databases, Genetic</term><term>Databases, Protein</term><term>Exons</term><term>Internet</term><term>Muramidase (chemistry)</term><term>Nucleic Acid Conformation</term><term>Phylogeny</term><term>Protein Folding</term><term>Proteins</term><term>RNA (chemistry)</term><term>Sequence Alignment</term><term>Sequence Analysis, Protein</term><term>Software</term><term>User-Computer Interface</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>DNA</term><term>Muramidase</term><term>RNA</term></keywords><keywords scheme="MESH" qualifier="instrumentation" xml:lang="en"><term>Computational Biology</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Computational Biology</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Computer Graphics</term><term>Database Management Systems</term><term>Databases, Genetic</term><term>Databases, Protein</term><term>Exons</term><term>Internet</term><term>Nucleic Acid Conformation</term><term>Phylogeny</term><term>Protein Folding</term><term>Proteins</term><term>Sequence Alignment</term><term>Sequence Analysis, Protein</term><term>Software</term><term>User-Computer Interface</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Friend is a bioinformatics application designed for simultaneous analysis and visualization of multiple structures and sequences of proteins and/or DNA/RNA. The application provides basic functionalities, such as structure visualization, with different rendering and coloring, sequence alignment and simple phylogeny analysis, along with a number of extended features to perform more complex analyses of sequence structure relationships, including structural alignment of proteins, investigation of specific interaction motifs, studies of protein-protein and protein-DNA interactions and protein super-families. It is also useful for functional annotation of proteins, protein modeling and protein folding studies. Friend provides three levels of usage: (1) an extensive GUI for a scientist with no programming experience, (2) a command line interface for scripting for a scientist with some programming experience and (3) the ability to extend Friend with user written libraries for an experienced programmer. The application is linked and communicates with local and remote sequence and structure databases.</div></front></TEI><pubmed><MedlineCitation Owner="NLM" Status="MEDLINE"><PMID Version="1">16076889</PMID><DateCreated><Year>2005</Year><Month>09</Month><Day>01</Day></DateCreated><DateCompleted><Year>2005</Year><Month>11</Month><Day>23</Day></DateCompleted><DateRevised><Year>2013</Year><Month>05</Month><Day>20</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Print">1367-4803</ISSN><JournalIssue CitedMedium="Print"><Volume>21</Volume><Issue>18</Issue><PubDate><Year>2005</Year><Month>Sep</Month><Day>15</Day></PubDate></JournalIssue><Title>Bioinformatics (Oxford, England)</Title><ISOAbbreviation>Bioinformatics</ISOAbbreviation></Journal><ArticleTitle>Friend, an integrated analytical front-end application for bioinformatics.</ArticleTitle><Pagination><MedlinePgn>3677-8</MedlinePgn></Pagination><Abstract><AbstractText Label="UNLABELLED">Friend is a bioinformatics application designed for simultaneous analysis and visualization of multiple structures and sequences of proteins and/or DNA/RNA. The application provides basic functionalities, such as structure visualization, with different rendering and coloring, sequence alignment and simple phylogeny analysis, along with a number of extended features to perform more complex analyses of sequence structure relationships, including structural alignment of proteins, investigation of specific interaction motifs, studies of protein-protein and protein-DNA interactions and protein super-families. It is also useful for functional annotation of proteins, protein modeling and protein folding studies. Friend provides three levels of usage: (1) an extensive GUI for a scientist with no programming experience, (2) a command line interface for scripting for a scientist with some programming experience and (3) the ability to extend Friend with user written libraries for an experienced programmer. The application is linked and communicates with local and remote sequence and structure databases.</AbstractText><AbstractText Label="AVAILABILITY" NlmCategory="BACKGROUND">http://mozart.bio.neu.edu/friend.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Abyzov</LastName><ForeName>Alexej</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>Department of Biology, Northeastern University, Boston, MA, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Errami</LastName><ForeName>Mounir</ForeName><Initials>M</Initials></Author><Author ValidYN="Y"><LastName>Leslin</LastName><ForeName>Chesley M</ForeName><Initials>CM</Initials></Author><Author ValidYN="Y"><LastName>Ilyin</LastName><ForeName>Valentin A</ForeName><Initials>VA</Initials></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2005</Year><Month>08</Month><Day>02</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>Bioinformatics</MedlineTA><NlmUniqueID>9808944</NlmUniqueID><ISSNLinking>1367-4803</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D011506">Proteins</NameOfSubstance></Chemical><Chemical><RegistryNumber>63231-63-0</RegistryNumber><NameOfSubstance UI="D012313">RNA</NameOfSubstance></Chemical><Chemical><RegistryNumber>9007-49-2</RegistryNumber><NameOfSubstance UI="D004247">DNA</NameOfSubstance></Chemical><Chemical><RegistryNumber>EC 3.2.1.17</RegistryNumber><NameOfSubstance UI="D009113">Muramidase</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName MajorTopicYN="N" UI="D019295">Computational Biology</DescriptorName><QualifierName MajorTopicYN="N" UI="Q000295">instrumentation</QualifierName><QualifierName MajorTopicYN="Y" UI="Q000379">methods</QualifierName></MeshHeading><MeshHeading><DescriptorName MajorTopicYN="N" UI="D003196">Computer Graphics</DescriptorName></MeshHeading><MeshHeading><DescriptorName MajorTopicYN="N" UI="D004247">DNA</DescriptorName><QualifierName MajorTopicYN="N" UI="Q000737">chemistry</QualifierName></MeshHeading><MeshHeading><DescriptorName MajorTopicYN="N" UI="D003628">Database Management Systems</DescriptorName></MeshHeading><MeshHeading><DescriptorName MajorTopicYN="N" UI="D030541">Databases, Genetic</DescriptorName></MeshHeading><MeshHeading><DescriptorName MajorTopicYN="N" UI="D030562">Databases, Protein</DescriptorName></MeshHeading><MeshHeading><DescriptorName MajorTopicYN="N" UI="D005091">Exons</DescriptorName></MeshHeading><MeshHeading><DescriptorName MajorTopicYN="N" UI="D020407">Internet</DescriptorName></MeshHeading><MeshHeading><DescriptorName MajorTopicYN="N" UI="D009113">Muramidase</DescriptorName><QualifierName MajorTopicYN="N" UI="Q000737">chemistry</QualifierName></MeshHeading><MeshHeading><DescriptorName MajorTopicYN="N" UI="D009690">Nucleic Acid Conformation</DescriptorName></MeshHeading><MeshHeading><DescriptorName MajorTopicYN="N" UI="D010802">Phylogeny</DescriptorName></MeshHeading><MeshHeading><DescriptorName MajorTopicYN="N" UI="D017510">Protein Folding</DescriptorName></MeshHeading><MeshHeading><DescriptorName MajorTopicYN="N" UI="D011506">Proteins</DescriptorName></MeshHeading><MeshHeading><DescriptorName MajorTopicYN="N" UI="D012313">RNA</DescriptorName><QualifierName MajorTopicYN="N" UI="Q000737">chemistry</QualifierName></MeshHeading><MeshHeading><DescriptorName MajorTopicYN="N" UI="D016415">Sequence Alignment</DescriptorName></MeshHeading><MeshHeading><DescriptorName MajorTopicYN="N" UI="D020539">Sequence Analysis, Protein</DescriptorName></MeshHeading><MeshHeading><DescriptorName MajorTopicYN="Y" UI="D012984">Software</DescriptorName></MeshHeading><MeshHeading><DescriptorName MajorTopicYN="N" UI="D014584">User-Computer Interface</DescriptorName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="aheadofprint"><Year>2005</Year><Month>8</Month><Day>2</Day></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2005</Year><Month>8</Month><Day>4</Day><Hour>9</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2005</Year><Month>12</Month><Day>13</Day><Hour>9</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2005</Year><Month>8</Month><Day>4</Day><Hour>9</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pii">bti602</ArticleId><ArticleId IdType="doi">10.1093/bioinformatics/bti602</ArticleId><ArticleId IdType="pubmed">16076889</ArticleId></ArticleIdList></PubmedData></pubmed></record>Pour manipuler ce document sous Unix (Dilib)
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