Energy minimization Help
The PmiR-NA has many useful miRNA-target network analysis and functions that are demonstrated in this user guide. It is a web-based tool that aids analysis of miRNA targets and its interaction network. PmiR-NA is very easy to use, and provides an user-friendly interface.
a. Web browser with Adobe Flashplayer Plugin. Download Here
b. Input miRNA and target query sequence/files.
The Browse page mainly contains miRNAs information along with its experimentally validated targets, hybridization energy, abiotic stress details and its homologs. Here, the user need to first select the organism from the first dropdown menu. After organism selection, user can seen that there are two separate sections for the seach. In the first section, user can search by miRNA ID and in the second section user can search by miRNA sequence.
As the first toggle is clicked, user can see the dropdown menu having the list of validated miRNA IDs of the respective organism selected in the first dropdown menu. User need to select the miRNA ID to view the search results. As the miRNA ID is selected, it retrives information from the pmiR-NA database for a selected miRNA of the species of interest, and display the search results in a tabular form below the toggle option.
In the second section, user again have to specify the organism from the first dropdown menu. After organism selection, a name to the search sequence is to be provided by the user in the first input textbox and then user need to paste the miRNA sequence in the second input textbox. As the submit botton is clicked, the sequence homologs for the input sequence in second textbox are shown on the new result page in a tabular form. The result can also be downloaded by “click here” option to view output file.
The Networking page dynamically generate biological network of miRNA and their targets. To visualize the network user first need to select the organism from the dropdown menu. As the organism is selected, user must provide a name to the network in the first input textbox. After a name is given to the network that is going to be drawn, user needs to select the miRNA ID from the second dropdown menu which is the list of validated miRNA IDs of the selected organism from the first dropdown menu.
As the miRNA ID is submitted, a new result page is shown. The result page shows a adobe flashplayer plugin network frame and below the frame, a gene annotation table having list of targets and their interacting parters in the above network are shown. The network visualization is mainly done by using Cytoscape Web (http://cytoscapeweb.cytoscape.org/).
The full Cytoscape tutorial can be found here: http://www.cytoscape.org/documentation_users.html.
The network shows the single input, miRNA node in red color and its target nodes in sky-blue color. The edges from the miRNA which are connecting it to the first target are shown in red color. Further the targets connect to the interacting targets with an edges having blue color. The nodes in the network can be draged by the user anywhere inside the network frame. User can also maximize and minimize the network inside the frame by increasing or decreasing the size using the pan zoom control panel placed on the bottom left corner of the network frame.
Each node (miRNA, targets and its interacting parters) can select its first neighbors by the content menu option on right click, placed for each nodes. As the “Select first neighbors” option is clicked, the first neighbors of that node are highlighted. All the selected nodes in this case can also be moved within the network frame at the same time.
Another feature to be marked in the network drawn is to visualize the details about each node in the network frame itself. Here, user needs to move the cursor above a node to view the onmouse event feature which helps to shown the gene details along with the correlation coefficient, degree and betweenness of target nodes inside a yellow color box. As the cursor is on the node, not only the details of target node is shown in yellow box but the first neighbors of that particular nodes is also shown. Further if the user clicks on the target node, user will be linked to the webpage of UniprotKB showing the detailed information of the clicked target node. Similarly, if the user clicks on the miRNA node, one will be linked to a new webpage showing the details of miRNA-target hybridization energy (minimum free energy i.e mfe in kcal/mol) and secondary structure informations.
Further the network can also be customized by the user on changing the layout of the network using the dropdown menu placed at the top of the network frame. Force-directed layout is set as a default layout for the network but user can also change it to radial, circle or tree layouts. Beside the network layout dropdown menu, there are other customizable features for the user like “display labels” checkbox option to enable or disable the labels of the nodes to be viewed. User can also change the color of the network by “Change color” option placed below the network drawn. The user can download the network in output formats like SIF and GRAPHML formats. Further network statistics details can also be downloaded. In case the user customize the network using different features but wishes to revert back to the initial network, one can do so by using the “Relayout” option placed beside the “Display Labels” option. The gene annotation table shown below the network can also be downloaded in EXCEL format by clicking on the download image.
The user can also analyse the gene annotation list on the basis of target gene length by a click on the header to allow it to sort in an accending or desending order. Further the gene annotation details are linked to its reference webpages like Gene Ontology, Uniprot, KEGG, Gene ID, EnsemblGenomes.
For Predict Target page, user need to choose an organism within the list of nine organisms (Oryza sativa, Arabidopsis thaliana, Triticum aestivum, Zea mays, Physcomitrella patens, Hordeum vulgare, Sorghum bicolor, Populus trichocarpa and Medicago truncatula) from the first dropdown menu. After organism selection, user must select a prediction method within psRobot_v1.2 or TargetFinder_v1.6 from the second dropdown menu. Further user need to provide a name to the sequence in the first input textbox and then paste the query sequence in the second input textbox.
On submit, a new result webpage is shown on which a table having the list of predicted targets along with the prediction score are given. The predicted targets list can be analysed by clicking on the header of the table to sort accordingly. The output can also be downloaded by the “Output File” link. Both psRobot and TargetFinder are designed to find potential small RNA targets on a large scale.
The Hybridization Energy page looks for the energetically favorable interaction sites between a small RNA in a large RNA by using RNAhybrid. Hybridization energy page is mainly divided in two sections. The first section is used to search for the validated miRNA-target hybridization energy, which is pre-calculated and the second section is used to calculate the hybridization energy of the users query sequences.
In the first section, user needs to click on the toggle and choose an organism from the first dropdown menu. After that user must click on the next toggle to select the miRNA ID from the second dropdown menu and submit it.
The result is shown on a new webpage having a list of targets along with the length of target and miRNA sequence, minimum free energy (mfe), p-value, position, alignment and its secondary structure file in three formats i.e JPG, PS and PDF. User can view the JPG image on the same webpage itself by moving the cursor on the JPG link. A small window showing the secondary structure of the respective target along with its mfe in kcal/mol is shown as a image. The list of targets can be analysed by clicking the headers to sort the respective columns like mfe and p-value in either increasing or decreasing order. The result table can also be downloaded by clicking on the download image link.
In the second section, user can choose either of the two options between "Paste the fasta sequences" or "Upload the fasta files". Depending upon the choice of user, input miRNA and target sequences/files are provided. User can also provide various parameters for each hybridization energy calculation. In case user doesnot know about the parameters, one should simply provide the default parameters already written in the input textbox and hit submit.
The result of hybridization energy calculation is shown on a new webpage mostly in the similar way as the result of the first section. The result can also be downloaded by clicking on the download image.
The Abiotic Stress page provides the list of miRNA regulation in different plant abiotic stress conditions. This page is also divided in two separate sections i.e "Search by organism" and "Search by stress condition".
In the first section, user need to click the first toggle and choose the organism from the first dropdown menu. After organism selection, user need to select one choice between "Select miRNA ID" or "Select stress condition". Depending upon the user choice, one need to click the next toggle to select either miRNA ID or stress condition and hit submit.
After submit, user can view the results on new webpage showing the list of abiotic stress related details along with the miRNA expression pattern and the references which is hyperlinked.
In the second section, user need to click the second toggle i.e “Search by stress condition” and choose the aboitic stress condition from the dropdown menu and hit submit botton.
The result is shown on a new webpage containing the list of miRNA showing the selected stress condition which was given by the user. Here also the list is provided with the miRNA expression pattern and hyperlinked references.
Hello visitor, you have seen this page 1 times.
