GntR family of regulators in : a sequence and structure based characterization-4

<p><b>Copyright information:</b></p><p>Taken from "GntR family of regulators in : a sequence and structure based characterization"</p><p>http://www.biomedcentral.com/1471-2164/8/289</p><p>BMC Genomics 2007;8():289-289.</p><p>Published online 23 Aug 2007</p><p>PMCID:PMC2018728.</p><p></p> sequence alignment has been drawn. High and low consensus levels were fixed arbitrarily at 80% and 40% of identity and are represented respectively by the capital and lowercase letters. Consensus symbol ! used for anyone of IV; $ is anyone of LM; % is anyone of FY; # is anyone of NDQEBZ. In graphical representation α-helix region and β-sheet regions are highlighted with light and dark gray background

NetVA: an R package for network vulnerability and influence analysis

In biological network analysis, identifying key molecules plays a decisive role in the development of potential diagnostic and therapeutic candidates. Among various approaches of network analysis, network vulnerability analysis is quite important, as it assesses significant associations between topological properties and the functional essentiality of a network. Similarly, some node centralities are also used to screen out key molecules. Among these node centralities, escape velocity centrality (EVC), and its extended version (EVC+) outperform others, viz., Degree, Betweenness, and Clustering coefficient. Keeping this in mind, we aimed to develop a first-of-its-kind R package named NetVA, which analyzes networks to identify key molecular players (individual proteins and protein pairs/triplets) through network vulnerability and EVC+-based approaches. To demonstrate the application and relevance of our package in network analysis, previously published and publicly available protein–protein interactions (PPIs) data of human breast cancer were analyzed. This resulted in identifying some most important proteins. These included essential proteins, non-essential proteins, hubs, and bottlenecks, which play vital roles in breast cancer development. Thus, the NetVA package, available at https://github.com/kr-swapnil/NetVA with a detailed tutorial to download and use, assists in predicting potential candidates for therapeutic and diagnostic purposes by exploring various topological features of a disease-specific PPIs network. Communicated by Ramaswamy H. Sarma</p

GntR family of regulators in : a sequence and structure based characterization-5

<p><b>Copyright information:</b></p><p>Taken from "GntR family of regulators in : a sequence and structure based characterization"</p><p>http://www.biomedcentral.com/1471-2164/8/289</p><p>BMC Genomics 2007;8():289-289.</p><p>Published online 23 Aug 2007</p><p>PMCID:PMC2018728.</p><p></p> sequence alignment has been drawn. High and low consensus levels were fixed arbitrarily at 80% and 40% of identity and are represented respectively by the capital and lowercase letters. Consensus symbol ! used for anyone of IV; $ is anyone of LM; % is anyone of FY; # is anyone of NDQEBZ. In graphical representation α-helix region and β-sheet regions are highlighted with light and dark gray background

GntR family of regulators in : a sequence and structure based characterization-6

<p><b>Copyright information:</b></p><p>Taken from "GntR family of regulators in : a sequence and structure based characterization"</p><p>http://www.biomedcentral.com/1471-2164/8/289</p><p>BMC Genomics 2007;8():289-289.</p><p>Published online 23 Aug 2007</p><p>PMCID:PMC2018728.</p><p></p>ranched again into two groups (FadR and VanR). (Abbreviations are as indicated in Table 1 and Table 2)

GntR family of regulators in : a sequence and structure based characterization-1

<p><b>Copyright information:</b></p><p>Taken from "GntR family of regulators in : a sequence and structure based characterization"</p><p>http://www.biomedcentral.com/1471-2164/8/289</p><p>BMC Genomics 2007;8():289-289.</p><p>Published online 23 Aug 2007</p><p>PMCID:PMC2018728.</p><p></p> sequence alignment has been drawn. High and low consensus levels were fixed arbitrarily at 80% and 40% of identity and are represented respectively by the capital and lowercase letters. Consensus symbol ! used for anyone of IV; $ is anyone of LM; % is anyone of FY; # is anyone of NDQEBZ. In graphical representation α-helix region and β-sheet regions are highlighted with light and dark gray background

GntR family of regulators in : a sequence and structure based characterization-0

<p><b>Copyright information:</b></p><p>Taken from "GntR family of regulators in : a sequence and structure based characterization"</p><p>http://www.biomedcentral.com/1471-2164/8/289</p><p>BMC Genomics 2007;8():289-289.</p><p>Published online 23 Aug 2007</p><p>PMCID:PMC2018728.</p><p></p>ranched again into two groups (FadR and VanR). (Abbreviations are as indicated in Table 1 and Table 2)

GntR family of regulators in : a sequence and structure based characterization-3

<p><b>Copyright information:</b></p><p>Taken from "GntR family of regulators in : a sequence and structure based characterization"</p><p>http://www.biomedcentral.com/1471-2164/8/289</p><p>BMC Genomics 2007;8():289-289.</p><p>Published online 23 Aug 2007</p><p>PMCID:PMC2018728.</p><p></p> sequence alignment has been drawn. High and low consensus levels were fixed arbitrarily at 80% and 40% of identity and are represented respectively by the capital and lowercase letters. Consensus symbol ! used for anyone of IV; $ is anyone of LM; % is anyone of FY; # is anyone of NDQEBZ. In graphical representation α-helix region and β-sheet regions are highlighted with light and dark gray background

GntR family of regulators in : a sequence and structure based characterization-2

<p><b>Copyright information:</b></p><p>Taken from "GntR family of regulators in : a sequence and structure based characterization"</p><p>http://www.biomedcentral.com/1471-2164/8/289</p><p>BMC Genomics 2007;8():289-289.</p><p>Published online 23 Aug 2007</p><p>PMCID:PMC2018728.</p><p></p> sequence alignment has been drawn. High and low consensus levels were fixed arbitrarily at 80% and 40% of identity and are represented respectively by the capital and lowercase letters. Consensus symbol ! used for anyone of IV; $ is anyone of LM; % is anyone of FY; # is anyone of NDQEBZ. In graphical representation α-helix region and β-sheet regions are highlighted with light and dark gray background

Flowchart of the methodology.

<p>Flowchart of the methodology.</p

A searchable mode to retrieve RBBHS and DNA motifs.

<p><b>A.</b> Interface to retrieve the RBBHs; <b>B.</b> Interface to retrieve the regulatory DNA motifs; <b>C.</b> Interface to retrieve the similar DNA motifs to the desired DNA sequence.</p