phage-phenomics-physiological-approaches-to-characterize-novel-viral

Phage Phenomics: Physiological Approaches to Characterize Novel Viral Proteins

Current investigations into phage-host interactions are dependent on extrapolating knowledge from (meta)genomes. Interestingly, 60 - 95% of all phage ...

San Diego State University

Minimally invasive valve replacement is limited to bioprosthetic aortic and pulmonary valves for use in very specific populations of patients. Replacement via trans-catheter and transapical techniques should be used only in patients in whom traditional surgical replacement is deemed an unacceptable risk. Nursing management will focus heavily on care for comorbid conditions because of the high-risk nature of the patients in whom these valves will initially be implanted.

Transcatheter and transapical aortic valve replacement.

Mutations that arise in HIV-1 protease after exposure to various HIV-1 protease inhibitors have proved to be a difficult aspect in the treatment of HIV. Mutations in the binding pocket of the protease can prevent the protease inhibitor from binding to the protein effectively. In the present study, the crystal structures of 68 HIV-1 proteases complexed with one of the nine FDA approved protease inhibitors from the Protein Data Bank (PDB) were analyzed by (a) identifying the mutational changes with the aid of a developed mutation map and (b) correlating the structure of the binding pockets with the complexed inhibitors. The mutations of each crystal structure were identified by comparing the amino acid sequence of each structure against the HIV-1 wild-type strain HXB2. These mutations were visually presented in the form of a mutation map to analyze mutation patterns corresponding to each protease inhibitor. The crystal structure mutation patterns of each inhibitor (in vitro) were compared against the mutation patterns observed in in vivo data. The in vitro mutation patterns were found to be representative of most of the major in vivo mutations. We then performed a data mining analysis of the binding pockets from each crystal structure in terms of their chemical descriptors to identify important structural features of the HIV-1 protease protein with respect to the binding conformation of the HIV-1 protease inhibitors. Data mining analysis is performed using several classification techniques: Random Forest (RF), linear discriminant analysis (LDA), and logistic regression (LR). We developed two hybrid models, RF-LDA and RF-LR. Random Forest is used as a feature selection proxy, reducing the descriptor space to a few of the most relevant descriptors determined by the classifier. These descriptors are then used to develop the subsequent LDA, LR, and hierarchical classification models. Clustering analysis of the binding pockets using the selected descriptors used to produce the optimal classification models reveals conformational similarities of the ligands in each cluster. This study provides important information in understanding the structural features of HIV-1 protease which cannot be studied by other existing in vivo genomic data sets.

Computational analysis of HIV-1 protease protein binding pockets.

&#x52A8;&#x673A;&#xFF1A; &#x566C;&#x83CC;&#x4F53;&#x6709;&#x4E24;&#x79CD;&#x622A;&#x7136;&#x4E0D;&#x540C;&#x7684;&#x751F;&#x6D3B;&#x65B9;&#x5F0F;&#xFF1A; &#x6076;&#x6BD2;&#x548C;&#x6E29;&#x5E26;&#x3002;&#x6076;&#x6BD2;&#x7684;&#x751F;&#x6D3B;&#x65B9;&#x5F0F;&#x6709;&#x5F88;&#x591A;&#x5F71;&#x54CD;&#x566C;&#x83CC;&#x4F53;&#x7597;&#x6CD5;&#x3001; &#x57FA;&#x56E0;&#x7EC4;&#x5B66;&#x548C;&#x5FAE;&#x751F;&#x7269;&#x5B66;&#x3002;&#x786E;&#x5B9A;&#x5F53;&#x524D;&#x4F7F;&#x7528;&#x6807;&#x51C6;&#x683D;&#x57F9;&#x6280;&#x672F;&#x786E;&#x5B9A;&#x65B0;&#x987A;&#x5E8F;&#x7684;&#x566C;&#x83CC;&#x4F53;&#x5206;&#x4E3A;&#x54EA;&#x4E9B;&#x751F;&#x6D3B;&#x65B9;&#x5F0F;&#x3002;&#x8FD9;&#x79CD;&#x5B9E;&#x9A8C;&#x5BA4;&#x5DE5;&#x4F5C;&#x4E0D;&#x4EC5;&#x6210;&#x672C;&#x9AD8;&#x6602;&#xFF0C;&#x800C;&#x4E14;&#x8017;&#x8D39;&#x65F6;&#x95F4;&#xFF0C;&#x4F46;&#x4E5F;&#x4E0D;&#x80FD;&#x7528;&#x566C;&#x83CC;&#x4F53;&#x57FA;&#x56E0;&#x7EC4;&#x4ECE;&#x73AF;&#x5883;&#x6D4B;&#x5E8F;&#x6784;&#x9020;&#x4E0A;&#x3002;&#x56E0;&#x6B64;&#x9700;&#x8981;&#x4E00;&#x79CD;&#x8BA1;&#x7B97;&#x65B9;&#x6CD5;&#xFF0C;&#x5B83;&#x5229;&#x7528;&#x566C;&#x83CC;&#x4F53;&#x57FA;&#x56E0;&#x7EC4;&#x7684;&#x5E8F;&#x5217;&#x6570;&#x636E;&#x3002;&#x7ED3;&#x679C;&#xFF1A; PHACTS &#x5229;&#x7528;&#x4E00;&#x79CD;&#x65B0;&#x578B;&#x7684;&#x76F8;&#x4F3C;&#x6027;&#x7B97;&#x6CD5;&#x548C;&#x76D1;&#x7763;&#x7684;&#x968F;&#x673A;&#x68EE;&#x6797;&#x5206;&#x7C7B;&#x5668;&#x6765;&#x4F5C;&#x4E00;&#x4E2A;&#x9884;&#x6D4B;&#xFF0C;&#x566C;&#x83CC;&#x4F53;&#xFF0C;&#x7531;&#x5176;&#x86CB;&#x767D;&#x8D28;&#x7EC4;&#x5B66;&#xFF0C;&#x63CF;&#x8FF0;&#x7684;&#x751F;&#x6D3B;&#x65B9;&#x5F0F;&#x662F;&#x6BD2;&#x8FD8;&#x662F;&#x6E29;&#x5E26;&#x3002;&#x76F8;&#x4F3C;&#x6027;&#x7B97;&#x6CD5;&#x521B;&#x5EFA;&#x8BBE;&#x7F6E;&#x4ECE;&#x566C;&#x83CC;&#x4F53;&#x4E0E;&#x5DF2;&#x77E5;&#x7684;&#x751F;&#x6D3B;&#x65B9;&#x5F0F;&#x548C;&#x751F;&#x6D3B;&#x65B9;&#x5F0F;&#x7684;&#x6CE8;&#x91CA;&#xFF0C;&#x4EE5;&#x53CA;&#x5217;&#x8F66;&#x968F;&#x673A;&#x68EE;&#x6797;&#x8FDB;&#x884C;&#x5206;&#x7C7B;&#x7684;&#x566C;&#x83CC;&#x4F53;&#x7684;&#x751F;&#x6D3B;&#x65B9;&#x5F0F;&#x7684;&#x57F9;&#x8BAD;&#x3002;PHACTS &#x9884;&#x6D4B;&#x90FD;&#x8868;&#x73B0;&#x51FA; 99%&#x7684;&#x7CBE;&#x786E;&#x7387;&#x3002;&#x53EF;&#x7528;&#x6027;&#x548C;&#x6267;&#x884C;&#x60C5;&#x51B5;&#xFF1A; PHACTS &#x5728; PERL &#x7F16;&#x7A0B;&#x8BED;&#x8A00;&#x548C;&#x5229;&#x7528; [29] &#x7684;&#x5BB6;&#x4F19;&#x7A0B;&#x5E8F;&#x548C;&#x7F16;&#x7A0B;&#x8BED;&#x8A00;&#x5E93;&quot;&#x968F;&#x673A;&#x68EE;&#x6797;&quot;[30] &#x7684;&#x7814;&#x53D1;&#x3002;PHACTS &#x8F6F;&#x4EF6;&#x662F;&#x5F00;&#x653E;&#x6E90;&#x4EE3;&#x7801;&#x548C;&#x4F5C;&#x4E3A;&#x53EF;&#x4E0B;&#x8F7D;&#x7684;&#x72EC;&#x7ACB;&#x7248;&#x672C;&#x53EF;&#x7528;&#x6216;&#x53EF;&#x5728;&#x7EBF;&#x8BBF;&#x95EE;&#x4F5C;&#x4E3A;&#x4E00;&#x4E2A;&#x7528;&#x6237;&#x53CB;&#x597D;&#x7684; web &#x754C;&#x9762;&#x3002;&#x6E90;&#x4EE3;&#x7801;&#x3001; &#x5E2E;&#x52A9;&#x6587;&#x4EF6;&#x548C;&#x5728;&#x7EBF;&#x7248;&#x672C;&#x53D1;&#x552E; http://www.phantome.org/PHACTS/&#x3002;&#x8054;&#x7CFB;&#x4EBA;&#xFF1A; katelyn@rohan.sdsu.edu*&#x3001; redwards@sciences.sdsu.edu*

PHACTS&#xFF0C;&#x8BA1;&#x7B97;&#x65B9;&#x6CD5;&#x5206;&#x7C7B;&#x7684;&#x566C;&#x83CC;&#x4F53;&#x7684;&#x751F;&#x6D3B;&#x65B9;&#x5F0F;&#x3002;

MOTIVATION: Bacteriophages have two distinct lifestyles: virulent and temperate. The virulent lifestyle has many implications for phage therapy, genomics, and microbiology. Determining which lifestyle a newly sequenced phage falls into is currently determined using standard culturing techniques. Such laboratory work is not only costly and time consuming, but also cannot be used on phage genomes constructed from environmental sequencing. Therefore a computational method that utilizes the sequence data of phage genomes is needed. RESULTS: PHACTS utilizes a novel similarity algorithm and a supervised Random Forest classifier to make a prediction whether the lifestyle of a phage, described by its proteome, is virulent or temperate. The similarity algorithm creates a training set from phages with known lifestyles and along with the lifestyle annotation, trains a Random Forest to classify the lifestyle of a phage. PHACTS predictions are shown to have a 99% precision rate.Availability and Implementation: PHACTS was implemented in the PERL programming language and utilizes the FASTA program [29] and the R programming language library "Random Forest" [30]. The PHACTS software is open source and is available as downloadable stand-alone version or can be accessed online as a user-friendly web interface. The source code, help files and online version are available at http://www.phantome.org/PHACTS/. CONTACT: katelyn@rohan.sdsu.edu*, redwards@sciences.sdsu.edu*

PHACTS, a computational approach to classifying the lifestyle of phages.

MOTIVATION: Les bact&#xE9;riophages ont deux modes de vie distincts: virulentes et temp&#xE9;r&#xE9;es. Le mode de vie virulente a de nombreuses implications pour th&#xE9;rapie par les phages, la g&#xE9;nomique et microbiologie. D&#xE9;terminer quels style de vie d&#x26;#39;un phage nouvellement s&#xE9;quenc&#xE9; tombe dans est actuellement d&#xE9;termin&#xE9;e en utilisant des techniques de culture standard. Travaux de laboratoire tel n&#x26;#39;est pas seulement co&#xFB;teux en temps et, mais aussi ne peut pas &#xEA;tre utilis&#xE9; sur les g&#xE9;nomes de phages construites &#xE0; partir de s&#xE9;quen&#xE7;age de l&#x26;#39;environnement. Par cons&#xE9;quent, une m&#xE9;thode de calcul qui utilise les donn&#xE9;es de s&#xE9;quence de g&#xE9;nomes de phages est n&#xE9;cessaire. R&#xC9;SULTATS: PHACTS utilise un algorithme de similarit&#xE9; roman et un classificateur supervis&#xE9; la for&#xEA;t au hasard pour faire une pr&#xE9;diction si le mode de vie d&#x26;#39;un phage, d&#xE9;crit par son prot&#xE9;ome, est virulente ou temp&#xE9;r&#xE9;e. L&#x26;#39;algorithme de similitude cr&#xE9;e un ensemble de formation de phages avec un mode de vie connues et avec l&#x26;#39;annotation mode de vie, forme une for&#xEA;t al&#xE9;atoire de classer le style de vie d&#x26;#39;un phage. Pr&#xE9;dictions PHACTS sont montr&#xE9; pour avoir un rate.Availability pr&#xE9;cision de 99% et mise en &#x153;uvre: PHACTS a &#xE9;t&#xE9; mis en &#x153;uvre dans le langage de programmation PERL et utilise le programme FASTA [29] et la biblioth&#xE8;que R langage de programmation &#x26;quot;For&#xEA;t au hasard&#xBB; [30]. Le logiciel PHACTS est open source et est disponible en t&#xE9;l&#xE9;chargement version stand-alone ou peut &#xEA;tre consult&#xE9; en ligne comme une interface Web conviviale. Le code source, fichiers d&#x26;#39;aide et la version en ligne sont disponibles &#xE0; http://www.phantome.org/PHACTS/. PERSONNE-RESSOURCE: katelyn@rohan.sdsu.edu *, * redwards@sciences.sdsu.edu

PHACTS, une approche computationnelle de classer le mode de vie des phages

MOTIVATION: Bakteriophagen haben zwei unterschiedliche Lebensstile: virulent und gem&auml;&szlig;igt. Der virulente Lebensstil hat viele Auswirkungen auf die Phagentherapie, Genomik und Mikrobiologie. Bestimmen, welcher Lebensstil eine neu sequenzierte Phage f&auml;llt derzeit bestimmt wird mit standard-culturing-Techniken. Solche Laborarbeit ist nicht nur kostspielig und zeitaufw&auml;ndig, aber auch nicht verwendet werden, auf Phage Genome aus &ouml;kologischen Sequenzierung gebaut. Daher ist eine computational Methode, die die Sequenzdaten Phage Genome nutzt ben&ouml;tigt. Ergebnisse: PHACTS nutzt eine neuartige &Auml;hnlichkeit-Algorithmus und einer beaufsichtigten Random Forest-Klassifizierung, eine Vorhersage zu treffen, ob der Lebensstil der ein Phage, beschrieben durch seine Proteome virulenten oder gem&auml;&szlig;igt ist. Der &Auml;hnlichkeit-Algorithmus erstellt eine Ausbildung von Phagen mit bekannten Lebensstile und zusammen mit der Anmerkung Lebensstil Z&uuml;ge ein Random Forest, den Lebensstil der ein Phage zu klassifizieren. PHACTS Vorhersagen werden gezeigt, um eine zu 99 % Genauigkeit erzielen.Verf&uuml;gbarkeit und Umsetzung: PHACTS wurde in der Programmiersprache PERL implementiert und nutzt das FASTA-Programm [29] und das R Programmierung Sprache Bibliothek &quot;Random Forest&quot; [30]. Die PHACTS-Software ist open Source und ist als Stand-Alone-Version zum Herunterladen erh&auml;ltlich oder kann online abgerufen werden wie eine benutzerfreundliche Web-Oberfl&auml;che. Der Quellcode, Hilfedateien und online-Version stehen unter http://www.phantome.org/PHACTS/ zur Verf&uuml;gung. Kontakt: katelyn@rohan.sdsu.edu*, redwards@sciences.sdsu.edu*

PHACTS, ein computational Ansatz zur Klassifizierung des Lebensstils der Phagen.

MOTIVAZIONE: Batteriofagi hanno due stili distinti: virulenti e temperati. Lo stile di vita virulento ha molte implicazioni per la terapia dei fagi, genomica e microbiologia. Determinare quale stile di vita un fago appena sequenziato cade in &egrave; attualmente determinato utilizzando tecniche di coltura standard. Tale lavoro di laboratorio non &egrave; solo costoso e richiede tempo, ma non pu&ograve; essere utilizzato anche su genomes dei fagi costruito dal sequenziamento ambientale. &Egrave; pertanto necessario un metodo di calcolo che utilizza i dati di sequenza del genoma del fago. RISULTATI: PHACTS utilizza un algoritmo di romanzo somiglianza e un classificatore Random Forest sorvegliato per fare una previsione, se lo stile di vita di un fago, descritto dal suo proteoma &egrave; virulento o temperato. L&#39;algoritmo di somiglianza crea un allenamento impostato da fagi con noti stili di vita e insieme con l&#39;annotazione di lifestyle, treni una foresta Random per classificare lo stile di vita di un fago. Previsioni PHACTS sono dimostrate di avere un tasso di precisione del 99%.Disponibilit&agrave; e implementazione: PHACTS &egrave; stato implementato il linguaggio di programmazione Perl e utilizza il programma FASTA [29] e la R programming language library &quot;Random Forest&quot; [30]. Il software PHACTS &egrave; open source ed &egrave; disponibile in versione stand-alone scaricabile o accessibili on-line come un interfaccia web user-friendly. Il codice sorgente, file di aiuto e versione online sono disponibili presso http://www.phantome.org/PHACTS/. Contatti: katelyn@rohan.sdsu.edu*, redwards@sciences.sdsu.edu*

PHACTS, un approccio computazionale per classificare lo stile di vita dei fagi.

&#x52D5;&#x6A5F;&#xFF1A;&#x75C5;&#x539F;&#x6027;&#x3068;&#x6E29;&#x5E2F;&#xFF1A;&#x30D0;&#x30AF;&#x30C6;&#x30EA;&#x30AA;&#x30D5;&#x30A1;&#x30FC;&#x30B8;&#x306F;&#x3001;&#x4E8C;&#x3064;&#x306E;&#x7570;&#x306A;&#x308B;&#x30E9;&#x30A4;&#x30D5;&#x30B9;&#x30BF;&#x30A4;&#x30EB;&#x3092;&#x6301;&#x3063;&#x3066;&#x3044;&#x307E;&#x3059;&#x3002;&#x75C5;&#x539F;&#x6027;&#x306E;&#x30E9;&#x30A4;&#x30D5;&#x30B9;&#x30BF;&#x30A4;&#x30EB;&#x306F;&#x3001;&#x30D5;&#x30A1;&#x30FC;&#x30B8;&#x7642;&#x6CD5;&#x3001;&#x30B2;&#x30CE;&#x30DF;&#x30AF;&#x30B9;&#x3001;&#x304A;&#x3088;&#x3073;&#x5FAE;&#x751F;&#x7269;&#x5B66;&#x306E;&#x305F;&#x3081;&#x306E;&#x591A;&#x304F;&#x306E;&#x610F;&#x5473;&#x3092;&#x6301;&#x3063;&#x3066;&#x3044;&#x307E;&#x3059;&#x3002;&#x65B0;&#x305F;&#x306B;&#x914D;&#x5217;&#x6C7A;&#x5B9A;&#x3055;&#x30D5;&#x30A1;&#x30FC;&#x30B8;&#x304C;&#x3069;&#x308C;&#x306B;&#x8A72;&#x5F53;&#x3059;&#x308B;&#x30E9;&#x30A4;&#x30D5;&#x30B9;&#x30BF;&#x30A4;&#x30EB;&#x3092;&#x6C7A;&#x5B9A;&#x3059;&#x308B;&#x3068;&#x3001;&#x73FE;&#x5728;&#x6A19;&#x6E96;&#x7684;&#x306A;&#x57F9;&#x990A;&#x6280;&#x8853;&#x3092;&#x7528;&#x3044;&#x3066;&#x6C7A;&#x5B9A;&#x3055;&#x308C;&#x308B;&#x3002;&#x3053;&#x306E;&#x3088;&#x3046;&#x306A;&#x5B9F;&#x9A13;&#x5BA4;&#x3067;&#x306E;&#x4F5C;&#x696D;&#x306F;&#x3001;&#x30B3;&#x30B9;&#x30C8;&#x3068;&#x6642;&#x9593;&#x304C;&#x304B;&#x304B;&#x308B;&#x3060;&#x3051;&#x3067;&#x306A;&#x304F;&#x3001;&#x74B0;&#x5883;&#x306E;&#x30B7;&#x30FC;&#x30AF;&#x30A8;&#x30F3;&#x30B7;&#x30F3;&#x30B0;&#x304B;&#x3089;&#x69CB;&#x7BC9;&#x30D5;&#x30A1;&#x30FC;&#x30B8;&#x306E;&#x30B2;&#x30CE;&#x30E0;&#x3067;&#x306F;&#x4F7F;&#x7528;&#x3067;&#x304D;&#x307E;&#x305B;&#x3093;&#x3002;&#x3057;&#x305F;&#x304C;&#x3063;&#x3066;&#x3001;&#x30D5;&#x30A1;&#x30FC;&#x30B8;&#x30B2;&#x30CE;&#x30E0;&#x306E;&#x914D;&#x5217;&#x30C7;&#x30FC;&#x30BF;&#x3092;&#x5229;&#x7528;&#x3057;&#x305F;&#x8A08;&#x7B97;&#x6CD5;&#x304C;&#x5FC5;&#x8981;&#x3068;&#x306A;&#x308A;&#x307E;&#x3059;&#x3002;&#x7D50;&#x679C;&#xFF1A;PHACTS&#x5C0F;&#x8AAC;&#x306E;&#x985E;&#x4F3C;&#x6027;&#x30A2;&#x30EB;&#x30B4;&#x30EA;&#x30BA;&#x30E0;&#x3068;&#x305D;&#x306E;&#x30D7;&#x30ED;&#x30C6;&#x30AA;&#x30FC;&#x30E0;&#x306B;&#x3088;&#x3063;&#x3066;&#x8A18;&#x8FF0;&#x3055;&#x308C;&#x305F;&#x30D5;&#x30A1;&#x30FC;&#x30B8;&#x306E;&#x30E9;&#x30A4;&#x30D5;&#x30B9;&#x30BF;&#x30A4;&#x30EB;&#x306F;&#x3001;&#x6BD2;&#x6027;&#x3084;&#x6E29;&#x5E2F;&#x3067;&#x3042;&#x308B;&#x304B;&#x3069;&#x3046;&#x304B;&#x306E;&#x4E88;&#x6E2C;&#x3092;&#x884C;&#x3046;&#x305F;&#x3081;&#x306E;&#x6559;&#x5E2B;&#x30E9;&#x30F3;&#x30C0;&#x30E0;&#x30D5;&#x30A9;&#x30EC;&#x30B9;&#x30C8;&#x5206;&#x985E;&#x3092;&#x63A1;&#x7528;&#x3057;&#x3066;&#x3044;&#x307E;&#x3059;&#x3002;&#x985E;&#x4F3C;&#x306E;&#x30A2;&#x30EB;&#x30B4;&#x30EA;&#x30BA;&#x30E0;&#x306F;&#x3001;&#x65E2;&#x77E5;&#x306E;&#x30E9;&#x30A4;&#x30D5;&#x30B9;&#x30BF;&#x30A4;&#x30EB;&#x3092;&#x6301;&#x3064;&#x3001;&#x30E9;&#x30A4;&#x30D5;&#x30B9;&#x30BF;&#x30A4;&#x30EB;&#x306E;&#x6CE8;&#x91C8;&#x3068;&#x3068;&#x3082;&#x306B;&#x30D5;&#x30A1;&#x30FC;&#x30B8;&#x304B;&#x3089;&#x30C8;&#x30EC;&#x30FC;&#x30CB;&#x30F3;&#x30B0;&#x30BB;&#x30C3;&#x30C8;&#x3092;&#x4F5C;&#x6210;&#x3057;&#x3001;&#x30D5;&#x30A1;&#x30FC;&#x30B8;&#x306E;&#x30E9;&#x30A4;&#x30D5;&#x30B9;&#x30BF;&#x30A4;&#x30EB;&#x3092;&#x5206;&#x985E;&#x3059;&#x308B;&#x305F;&#x3081;&#x306E;&#x30E9;&#x30F3;&#x30C0;&#x30E0;&#x30D5;&#x30A9;&#x30EC;&#x30B9;&#x30C8;&#x3092;&#x990A;&#x6210;&#x3059;&#x308B;&#x3002; PHACTS&#x4E88;&#x6E2C;&#x306F;99&#xFF05;&#x306E;&#x7CBE;&#x5EA6;rate.Availability&#x3068;&#x5B9F;&#x88C5;&#x3092;&#x6301;&#x3063;&#x3066;&#x3044;&#x308B;&#x3053;&#x3068;&#x304C;&#x793A;&#x3055;&#x308C;&#x3066;&#x3044;&#x307E;&#x3059;&#x3002;PHACTS&#x306F;Perl&#x30D7;&#x30ED;&#x30B0;&#x30E9;&#x30DF;&#x30F3;&#x30B0;&#x8A00;&#x8A9E;&#x3067;&#x5B9F;&#x88C5;&#x3055;&#x308C;&#x3001;FASTA&#x30D7;&#x30ED;&#x30B0;&#x30E9;&#x30E0;&#x3092;&#x5229;&#x7528;&#x3057;&#x305F;[29]&#x3068;R&#x30D7;&#x30ED;&#x30B0;&#x30E9;&#x30DF;&#x30F3;&#x30B0;&#x8A00;&#x8A9E;&#x306E;&#x30E9;&#x30A4;&#x30D6;&#x30E9;&#x30EA; &#x26;quot;&#x30E9;&#x30F3;&#x30C0;&#x30E0;&#x68EE;&#x26;quot; [30]&#x3055;&#x308C;&#x307E;&#x3057;&#x305F;&#x3002; PHACTS&#x30BD;&#x30D5;&#x30C8;&#x30A6;&#x30A7;&#x30A2;&#x306F;&#x30AA;&#x30FC;&#x30D7;&#x30F3;&#x30BD;&#x30FC;&#x30B9;&#x3067;&#x3042;&#x308A;&#x3001;&#x30C0;&#x30A6;&#x30F3;&#x30ED;&#x30FC;&#x30C9;&#x53EF;&#x80FD;&#x306A;&#x30B9;&#x30BF;&#x30F3;&#x30C9;&#x30A2;&#x30ED;&#x30F3;&#x30D0;&#x30FC;&#x30B8;&#x30E7;&#x30F3;&#x3068;&#x3057;&#x3066;&#x5229;&#x7528;&#x53EF;&#x80FD;&#x3067;&#x3042;&#x308B;&#x304B;&#x3001;&#x30E6;&#x30FC;&#x30B6;&#x30FC;&#x30D5;&#x30EC;&#x30F3;&#x30C9;&#x30EA;&#x30FC;&#x306A;&#x30A6;&#x30A7;&#x30D6;&#x30A4;&#x30F3;&#x30BF;&#x30FC;&#x30D5;&#x30A7;&#x30FC;&#x30B9;&#x3001;&#x30AA;&#x30F3;&#x30E9;&#x30A4;&#x30F3;&#x30A2;&#x30AF;&#x30BB;&#x30B9;&#x3059;&#x308B;&#x3053;&#x3068;&#x304C;&#x3067;&#x304D;&#x307E;&#x3059;&#x3002;&#x30BD;&#x30FC;&#x30B9;&#x30B3;&#x30FC;&#x30C9;&#x3001;&#x30D8;&#x30EB;&#x30D7;&#x30D5;&#x30A1;&#x30A4;&#x30EB;&#x3068;&#x30AA;&#x30F3;&#x30E9;&#x30A4;&#x30F3;&#x7248;&#x306F;http://www.phantome.org/PHACTS/&#x3067;&#x3054;&#x5229;&#x7528;&#x3044;&#x305F;&#x3060;&#x3051;&#x307E;&#x3059;&#x3002;&#x304A;&#x554F;&#x3044;&#x5408;&#x308F;&#x305B;&#x5148;&#xFF1A;katelyn@rohan.sdsu.edu *&#x3001;redwards@sciences.sdsu.edu *

PHACTS&#x3001;&#x30D5;&#x30A1;&#x30FC;&#x30B8;&#x306E;&#x30E9;&#x30A4;&#x30D5;&#x30B9;&#x30BF;&#x30A4;&#x30EB;&#x3092;&#x5206;&#x985E;&#x3059;&#x308B;&#x8A08;&#x7B97;&#x8AD6;&#x7684;&#x30A2;&#x30D7;&#x30ED;&#x30FC;&#x30C1;

&#xB3D9;&#xAE30; &#xBD80;&#xC5EC;: Bacteriophages&#xB294; &#xB450; &#xAC1C;&#xC758; &#xC11C;&#xB85C; &#xB2E4;&#xB978; &#xB77C;&#xC774;&#xD504; &#xC2A4;&#xD0C0;&#xC77C;: &#xC545;&#xC131; &#xBC0F; &#xC628;&#xB300;. &#xC545;&#xC131; &#xB77C;&#xC774;&#xD504; &#xC2A4;&#xD0C0;&#xC77C;&#xC5D0;&#xB294; &#xC0B4; &#xADE0; &#xC18C; &#xCE58;&#xB8CC;, &#xC720;&#xC804;&#xCCB4;&#xD559;, &#xBC0F; &#xBBF8;&#xC0DD;&#xBB3C;&#xD559;&#xC5D0; &#xB300; &#xD55C; &#xB9CE;&#xC740; &#xC758;&#xBBF8;&#xAC00; &#xC788;&#xC2B5;&#xB2C8;&#xB2E4;. &#xACB0;&#xC815; &#xD558;&#xB294; &#xB77C;&#xC774;&#xD504; &#xC2A4;&#xD0C0;&#xC77C;&#xC5D0; &#xBE60;&#xC9C0;&#xACE0; &#xC0C8;&#xB85C; &#xC2DC;&#xD000;&#xC2A4; &#xB41C; &#xC0B4; &#xADE0; &#xC18C; &#xD604;&#xC7AC; &#xD45C;&#xC900; &#xC790;&#xB780; &#xAE30;&#xC220;&#xC744; &#xC0AC;&#xC6A9; &#xD558; &#xC5EC; &#xACB0;&#xC815; &#xB429;&#xB2C8;&#xB2E4;. &#xC774; &#xAC19;&#xC740; &#xC2E4;&#xD5D8;&#xC2E4; &#xC791;&#xC5C5; &#xBFD0;&#xB9CC; &#xC544;&#xB2C8;&#xB77C; &#xB9CE;&#xC740; &#xBE44;&#xC6A9;&#xACFC; &#xC2DC;&#xAC04;&#xC774; &#xC18C;&#xBAA8; &#xD558;&#xC9C0;&#xB9CC; &#xB610;&#xD55C; &#xC0B4; &#xADE0; &#xC18C; &#xAC8C;&#xB188; &#xC2DC;&#xD000;&#xC2F1; &#xD658;&#xACBD;&#xC5D0;&#xC11C; &#xAC74;&#xC124;&#xC5D0; &#xC0AC;&#xC6A9;&#xD560; &#xC218; &#xC5C6;&#xC2B5;&#xB2C8;&#xB2E4;. &#xB530;&#xB77C;&#xC11C; &#xC0B4; &#xADE0; &#xC18C; &#xAC8C;&#xB188; &#xC2DC;&#xD000;&#xC2A4; &#xB370;&#xC774;&#xD130;&#xB97C; &#xD65C;&#xC6A9; &#xD558; &#xC5EC; &#xC804;&#xC0B0; &#xBA54;&#xC11C;&#xB4DC;&#xAC00; &#xD544;&#xC694; &#xD569;&#xB2C8;&#xB2E4;. &#xACB0;&#xACFC;: PHACTS &#xC18C;&#xC124; &#xC720;&#xC0AC;&#xC131; &#xC54C;&#xACE0;&#xB9AC;&#xC998; &#xBC0F; &#xC545;&#xC131; &#xB610;&#xB294; &#xC628;&#xB300;&#xC758; &#xD504;&#xB85C;&#xD14C;&#xC634;&#xC5D0; &#xC758;&#xD574; &#xC124;&#xBA85; &#xB41C; &#xC0B4; &#xADE0; &#xC18C;&#xC758; &#xB77C;&#xC774;&#xD504; &#xC2A4;&#xD0C0;&#xC77C; &#xC778;&#xC9C0; &#xC608;&#xCE21; &#xC218; &#xC788;&#xB3C4;&#xB85D; &#xAC10;&#xB3C5;&#xB41C; &#xC784;&#xC758; &#xC232; &#xBD84;&#xB958;&#xC790;&#xB97C; &#xC774;&#xC6A9; &#xD55C;&#xB2E4;. &#xC720;&#xC0AC;&#xC131; &#xC54C;&#xACE0;&#xB9AC;&#xC998; &#xD559;&#xC2B5; &#xD398;&#xC774;&#xC9C0; &#xC54C;&#xB824;&#xC9C4;&#xB41C; &#xB77C;&#xC774;&#xD504; &#xC2A4;&#xD0C0;&#xC77C;&#xACFC; &#xB77C;&#xC774;&#xD504; &#xC2A4;&#xD0C0;&#xC77C; &#xC8FC;&#xC11D; &#xD568;&#xAED8; &#xC5F4;&#xCC28;&#xB294; &#xC0B4; &#xADE0; &#xC18C;&#xC758; &#xB77C;&#xC774;&#xD504; &#xC2A4;&#xD0C0;&#xC77C;&#xC744; &#xBD84;&#xB958; &#xD558;&#xAE30; &#xC704;&#xD574; &#xC784;&#xC758; &#xC232;&#xC5D0;&#xC11C;&#xC5D0;&#xC11C; &#xC9D1;&#xD569;&#xC744; &#xB9CC;&#xB4ED;&#xB2C8;&#xB2E4;. PHACTS &#xC608;&#xCE21; 99% &#xC815;&#xBC00; &#xC18D;&#xB3C4; &#xD45C;&#xC2DC; &#xB429;&#xB2C8;&#xB2E4;.&#xAC00;&#xC6A9;&#xC131;&#xACFC; &#xAD6C;&#xD604;: PHACTS &#xD504;&#xB85C;&#xADF8;&#xB798;&#xBC0D; &#xC5B8;&#xC5B4; PERL&#xB85C; &#xAD6C;&#xD604; &#xB41C; &#xBC0F; FASTA &#xD504;&#xB85C;&#xADF8;&#xB7A8; [29] &#xD504;&#xB85C;&#xADF8;&#xB798;&#xBC0D; &#xC5B8;&#xC5B4; &#xB77C;&#xC774;&#xBE0C;&#xB7EC;&#xB9AC; &quot;&#xC784;&#xC758; &#xC232;&quot; [30] R&#xC744; &#xC774;&#xC6A9; &#xD55C;&#xB2E4;. PHACTS &#xC18C;&#xD504;&#xD2B8;&#xC6E8;&#xC5B4;&#xB294; &#xC624;&#xD508; &#xC18C;&#xC2A4; &#xBC0F; &#xB2E4;&#xC6B4;&#xB85C;&#xB4DC; &#xAC00;&#xB2A5;&#xD55C; &#xB3C5;&#xB9BD; &#xC2E4;&#xD589;&#xD615; &#xBC84;&#xC804;&#xC73C;&#xB85C; &#xC0AC;&#xC6A9;&#xD560; &#xC218; &#xB610;&#xB294; &#xC628;&#xB77C;&#xC778;&#xC73C;&#xB85C; &#xC561;&#xC138;&#xC2A4;&#xD560; &#xC218; &#xC788;&#xB294; &#xC0AC;&#xC6A9;&#xC790; &#xCE5C;&#xD654;&#xC801;&#xC778; &#xC6F9; &#xC778;&#xD130;&#xD398;&#xC774;&#xC2A4;. &#xC18C;&#xC2A4; &#xCF54;&#xB4DC;, &#xB3C4;&#xC6C0;&#xB9D0; &#xD30C;&#xC77C; &#xBC0F; &#xC628;&#xB77C;&#xC778; &#xBC84;&#xC804; http://www.phantome.org/phacts/&#xC5D0;&#xC11C; &#xC0AC;&#xC6A9;&#xD560; &#xC218; &#xC788;&#xC2B5;&#xB2C8;&#xB2E4;. &#xC5F0;&#xB77D;&#xCC98;: katelyn@rohan.sdsu.edu*, redwards@sciences.sdsu.edu*

PHACTS, &#xBD84;&#xB958; &#xD398;&#xC774;&#xC9C0;&#xC758; &#xB77C;&#xC774;&#xD504; &#xC2A4;&#xD0C0;&#xC77C;&#xC5D0; &#xB300; &#xD55C; &#xC804;&#xC0B0; &#xC811;&#xADFC;.

MOTIVACI&#xD3;N: Los bacteri&#xF3;fagos tienen dos estilos de vida distintos: virulentas y templadas. El estilo de vida virulenta tiene muchas implicaciones para la terapia de fagos, la gen&#xF3;mica y la microbiolog&#xED;a. La determinaci&#xF3;n de qu&#xE9; estilo de vida de un fago nueva secuencia se divide en la actualidad se determin&#xF3; usando t&#xE9;cnicas est&#xE1;ndar de cultivo. Trabajo de laboratorio no s&#xF3;lo es costoso y consume tiempo, sino que adem&#xE1;s no se puede utilizar en genomas de fagos construidas a partir de la secuenciaci&#xF3;n del medio ambiente. Por lo tanto un m&#xE9;todo de c&#xE1;lculo que utiliza los datos de la secuencia de los genomas de fagos que se necesita. RESULTADOS: PHACTS utiliza un algoritmo de similitud novela y un clasificador supervisado Bosque aleatorio para hacer una predicci&#xF3;n de si el estilo de vida de un fago, descrito por su proteoma, es virulenta o templadas. El algoritmo de similitud crea un conjunto de entrenamiento de los fagos con estilos de vida conocidas y, junto con la anotaci&#xF3;n de estilo de vida, entrena a un bosque aleatorio para clasificar el estilo de vida de un fago. Predicciones PHACTS se demuestra que tienen una precisi&#xF3;n de 99% rate.Availability e Implementaci&#xF3;n: PHACTS fue implementado en el lenguaje de programaci&#xF3;n Perl y utiliza el programa FASTA [29] y la programaci&#xF3;n de R biblioteca para el lenguaje &#x26;quot;Bosque al azar&#x26;quot; [30]. El software PHACTS es open source y est&#xE1; disponible para su descarga en versi&#xF3;n stand-alone o puede accederse en l&#xED;nea como una interfaz web f&#xE1;cil de usar. El c&#xF3;digo fuente, archivos de ayuda y la versi&#xF3;n en l&#xED;nea est&#xE1;n disponibles en http://www.phantome.org/PHACTS/. CONTACTO: katelyn@rohan.sdsu.edu *, * redwards@sciences.sdsu.edu

PHACTS, un enfoque computacional para clasificar el estilo de vida de los fagos

All sequence data contain inherent information that can be measured by Shannon's uncertainty theory. Such measurement is valuable in evaluating large data sets, such as metagenomic libraries, to prioritize their analysis and annotation, thus saving computational resources. Here, Shannon's index of complete phage and bacterial genomes was examined. The information content of a genome was found to be highly dependent on the genome length, GC content, and sequence word size. In metagenomic sequences, the amount of information correlated with the number of matches found by comparison to sequence databases. A sequence with more information (higher uncertainty) has a higher probability of being significantly similar to other sequences in the database. Measuring uncertainty may be used for rapid screening for sequences with matches in available database, prioritizing computational resources, and indicating which sequences with no known similarities are likely to be important for more detailed analysis.

Applying Shannon's information theory to bacterial and phage genomes and metagenomes.

Metagenomics is a primary tool for the description of microbial and viral communities. The sheer magnitude of the data generated in each metagenome makes identifying key differences in the function and taxonomy between communities difficult to elucidate. Here we discuss the application of seven different data mining and statistical analyses by comparing and contrasting the metabolic functions of 212 microbial metagenomes within and between 10 environments. Not all approaches are appropriate for all questions, and researchers should decide which approach addresses their questions. This work demonstrated the use of each approach: for example, random forests provided a robust and enlightening description of both the clustering of metagenomes and the metabolic processes that were important in separating microbial communities from different environments. All analyses identified that the presence of phage genes within the microbial community was a predictor of whether the microbial community was host-associated or free-living. Several analyses identified the subtle differences that occur with environments, such as those seen in different regions of the marine environment.

Multivariate analysis of functional metagenomes.

Cystic Fibrosis (CF) is a multi-systemic disease resulting from mutations in the Cystic Fibrosis Transmembrane Regulator (CFTR) gene and has major manifestations in the sino-pulmonary, and gastro-intestinal tracts. Clinical phenotypes were generated using 26 common clinical variables to generate classes that overlapped quantiles of lung function and were based on multiple aspects of CF systemic disease.

Article	Year
Transcatheter and transapical aortic valve replacement. Critical care nurse\| PubMed ID: 19182278	2009
Computational analysis of HIV-1 protease protein binding pockets. Journal of chemical information and modeling\| PubMed ID: 20925403	2010
PHACTS, a computational approach to classifying the lifestyle of phages. Bioinformatics (Oxford, England)\| PubMed ID: 22238260	2012
Applying Shannon's information theory to bacterial and phage genomes and metagenomes. Scientific reports\| PubMed ID: 23301154	2013
Multivariate analysis of functional metagenomes. Frontiers in genetics\| PubMed ID: 23579547	2013
Multidimensional clinical phenotyping of an adult cystic fibrosis patient population. PloS one\| PubMed ID: 25822311	2015

Barbara A. Bailey

Biography

JoVE Journal Publications

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