CoralmiR

CoralmiR is a sub-database of CoralBioinfo which provides user-friendly interface to access predicted coral miRNAs as well as their targeting sites. It integrates published mRNA and small RNA sequencing data, helping users identify biological targeting events in different coral species. Users are allowed to search for their interested coral miRNAs through various services, besides they can input their interested genes or miRNAs to retrieve a targeting information list.

DATABASE CONTENT

MySQL 5.7 is utilized as database. All data is stored in MySQL tables.

Basic information

Basic information of coral miRNAs is stored in Table info:

mirdeep2, miREvo and ViennaRNA were used for identification of known miRNA and prediction of novel miRNA.

miRNA-precursor pairs

The relationship among miRNAs and precursor in different coral species is stored in Table pair:

*The structure image of precursor contains mature miRNA sequence which is highlighted with red.

Genes

Table gene records basic information about miRNA-targeted genes/transcripts.

Targets

Table target demonstrates predicted miRNA targets on coral unigenes from PacBio sequencing:

*All targets were predicted by miRanda. Several result parameters generated by the software are not shown in the table above. You can see them in the introduction to target result pages ▼below.

Annotation

Coral unigenes were annotated by 7 databases: GO, KEGG, KOG, Nr, Nt, Pfam and Swiss-Prot. Here is the Venn graph illustrating statistics on miRNA targets annotation:

Sequences

miRNA sequences are stored in .FASTA files as well. NCBI-BLAST databases have been built for sequence alignment service.

WEB INTERFACE

The website is developed under the LEMP (Linux, Nginx, MySQL and PHP) stack. Web functions are implemented by PHP 7.2 while Nginx works as web server. All services can be deployed by Docker.

Service

SEARCH

This service supports searching for target information by species, miRNA or gene/transcript.

BROWSE

This service allows users to explore their interested data by clicking related buttons. This page might be recognized as statistics dashboard of CoralmiR to some extents.

When browsing by species, unidentified miRNAs with precursors found are black-marked and inaccessible.

BLAST

Sequenceserver is utilized as BLAST server. Front-end codes were modified for user experience improvement.

API

See CoralmiR API.

Result

The following will describe the Markdown template of each result page.

miRNA

• hairpin

x
​
# {info.name}
​
- **ID:** CMIR{info.id}
​
- **Origin:** {info.origin}
​
<!--This button will appear only if the precursor is known.--><a href="http://www.mirbase.org/textsearch.shtml?q={info.name}" class="button">Search in miRBase</a>
​
## Sequence
​
```
{info.seq}
```
​
​
​
## miRNA
​
| Species        | ID            | Name                                     |
| ------------- | ------------- | ---------------------------------------- |
| {pair.species} | `Unfound`     | {pair.mature}                            |
| {pair.species} | CMIR{info.id} | [{pair.mature}](../mature/{pair.mature}) |
| ...           | ...           | ...                                      |

• mature

x
# {info.name}
​
- **ID:** CMIR{info.id}
- **Origin:** {info.origin}
- **Precursor:** [{pair.hairpin}](../hairpin/{pair.hairpin})
​
<!--This button will appear only if the miRNA is known.--><a href="http://www.mirbase.org/textsearch.shtml?q={info.name}" class="button">Search in miRBase</a>
​
## Sequence
​
```
{info.seq}
```
​
​
​
## Structure
​
![](../struct/{pair.struct})
​
​
​
## Target Gene
​
| ID                                      | Species          | Gene                                                   | Position          |
| --------------------------------------- | --------------- | ------------------------------------------------------ | ----------------- |
| [CMT{target.id}](../target/{target.id}) | {target.species} | [{target.gene}](../gene/{base64_encoded(target.gene)}) | {target.Position} |
| ...                                     | ...             | ...                                                    | ...               |

• star

x
# {info.name}
​
- **ID:** CMIR{info.id}
- **Origin:** {info.origin}
- **Precursor:** [{pair.hairpin}](../hairpin/{pair.hairpin})
​
<a href="../mature/{pair.mature}" class="button">{pair.mature}</a>
​
## Sequence
​
```
{info.seq}
```

Target

x
# CMT {target.id}
#### Species
{target.species}
​
#### miRNA
​
[{target.miRNA}](../mature/{target.miRNA})
​
#### Gene
[{target.gene}](../gene/{base64_encoded(target.gene)})
​
****
​
#### Score
​
| TotScore          | TotEnergy          | MaxScore          | MaxEnergy          |
| ----------------- | ------------------ | ----------------- | ------------------ |
| {target.TotScore} | {target.TotEnergy} | {target.MaxScore} | {target.MaxEnergy} |
​
****
​
#### Alignment
​
```
{target.graph}
```
​
| Q/R       | Length(nt)    | Start           | End           | %        |
| --------- | ------------- | --------------- | ------------- | -------- |
| **miRNA** | {target.LenQ} | {target.Qstart} | {target.Qend} | {AlignQ} |
| **Gene**  | {target.LenR} | {target.Rstart} | {target.Rend} | {AlignR} |

Gene

x
# {gene.name}
​
- **Species:** {gene.species}
- **ID:** CMG{gene.id}
​
<!--There are 7 buttons labeled "GO", "KEGG", "KOG", "Nr", "Nt", "Pfam" and "SwissProt" for users to get details. If there are no annotation results for the gene in one database, corresponding button will be unclickable.-->
​
​
​
## miRNA Target
​
| Name                                       | Position          | TotScore          | TotEnergy          | Detail                                  |
| ------------------------------------------ | ----------------- | ----------------- | ------------------ | --------------------------------------- |
| [{target.miRNA}](../mature/{target.miRNA}) | {target.Position} | {target.TotScore} | {target.TotEnergy} | [CMT{target.id}](../target/{target.id}) |
| ...                                        | ...               | ...               | ...                | ...                                     |