FAQ/Help Database
What is and which are the search options?
The search function is a mechanism provided to help finding information about a specific piRNA. It offer these search options:
- by piRNA: Find a piRNA using the accessing code
- by Alignment: Results in all piRNAs that have alignments over the parameters filled in the form field
- by Cluster: Find all piRNA clusters inside the genomic coordinates filled in the form fileds
- by Associated Gene: Find all piRNAs that have alignments overlapping the specific gene of your interest
- Cross Codes: The feature will translate your piRNA identification and accession codes from other RNA databases to those codes we use on piRNAdb. Also provide a link to the information page of the piRNA of interest.
Figure: Search Options available to the user. Number 1 indicates the methods to use to find the desired information and piRNAs associated. Number 2 indicates the filtering options provided to the user.
By piRNA:
Users can use the example link to have a clue about the search system. The codes to find piRNAs follow this pattern: "organism-piR-number", like this, "hsa-piR-4346" stands for the piRNA 4346 of Homo sapiens.
The organism code are:
Figure: Search piRNA result sample
The figure above shows a sample result page with some informations like sequence of the piRNAs.
By Alignment
The fields found are references to the localization of the alignments of the piRNAs on the organism genome.
Figure: Search alignment result sample
How can I view the piRNA, cluster and another genomic informations?
On specific piRNA information page of interest, you can find alignments belong to it.
Especially in this section, you can note that exist multiple informations related to alignments. The item number 1, let you choose the build of organism genome that you want to see the alignments. Number 2, you can choose which chromosome you want to use as a filter to find your data. The box number 3 displays all the informations about the alignments, including start and end positions and related targets to it. More over, all columns data can be ordered just clicking on column title. On the fouth item, there is a pagination system that can be used easily to browse between informations pages.
Figure 001.Informations and alignments of this piRNA
In the case of a cluster, the informations are the same but with one difference, the link to genomic conext is unique and can be found on the general information section.
Figura 002. Cluster information
Can I download de database data?
Yes, we have a specific page, "Downloads", the data storaged in this database.
Figura 001. Download Options
In the section piRNAs, the user can download of every piRNA sequences of a specific organism.
In the section Alignment the user can get all the alignments associated whit any piRNA in the database.
In the section Dataset, essential informations about the datasets of piRNA sequences can be downloaded.
In the section Cluster , all piRNA and alignments about a specific cluster cand be found and downloaded.
File formats to download
The download file is compressed to gzip file, which consist of a .txt or .fasta.
But specific information about one piRNA that can be found on the piRNA page, just can be downloaded in .fasta format.
If I find a bug?
Please tell us where, when and how you get this error, it will be very important to make this database way better. You can find our e-mail in the “Contact” page.
Why this database data can be differente from another database?
Because of the methodology differences which dataset uses, and about the differences on the cluster formation methodologies.
How to use the CrossCodes feature
The cross databases codes offer a simple solution to the integration between access codes from another databases to our system. Developed to offer more informations related to piRNA of interest of user, due to the lack of several updates on other databases.
Figure 001.Cross codes form and informations
First, the item number 1 is a form that you can write all your access codes from another databases, which one has to be in a newline to properly function of the system. The number 2 indicate the resuts of our data proccessing, where the piRNA that exist on our database are shown with a link to it. And those that doesn’t exist on our database, by the different methodologies used, a information that this piRNA doesn’t on our system exist is shown.
Target Cloud system
A tag cloud is a method to show the more frequent and revelant word on any topic or text. We developed a tag cloud system similar to that we found on any traditional websites to show all genes that can be targets of a specific piRNA.
Representation of target cloud system
On the number 1 item, we can find all genes had piRNA alignments in overlap, the size and color of gene is based on the importance and quantity of alignments that this piRNA had. So, bigger and more strong colors indicates more relevance of it. On item number 2, it’s the colors and quantity of alignments that they represent.
