CoralSym

CoralSym is a sub-database of CoralBioinfo which publishes several novel Symbiodiniaceae miRNAs identified in four reef-building coral species. It integrates published Symbiodiniaceae genome with mRNA and small RNA sequencing data from coral, helping users identify potential cross-kingdom targeting events in different coral species. Users are allowed to search for their interested Symbiodiniaceae 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 Symbiodiniaceae miRNAs is stored in Table info:

miRDP2 and mirdeep2 were used for identification of novel miRNA.

miRNA-precursor pairs

The relationship among Symbiodiniaceae miRNA 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. See CoralGene for details.

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 CoralSym 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.

Browser

The Symbiodiniaceae genome browser is customized by GIVE.

API

See CoralSym API.

Result

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

miRNA

• hairpin

# {info.name}
​
- **ID:** CSMIR{info.id}
​
- **Origin:** {info.origin}
​
- **Species:** {pair.sym_sp}
​
- **Loci:** {pair.loci}:{pair.start}..{pair.end}({pair.strand})
​
​
​
## Sequence
​
```
{info.seq}
```
​
## miRNA
​
### {No}. [{pair.mature}](../mature/{pair.mature})
​
<a style="pointer-events: none;" class="button button-pill button-primary button-tiny">{pair.coral_sp}</a>
​
![](../struct/{pair.hairpin}_{pair.mature}.png)

• mature

# {info.name}
​
- **ID:** CSMIR{info.id}
- **Origin:** {info.origin}
​
​
​
## Sequence
​
```
{info.seq}
```
​
## Precursor
​
| Name                                        | Species        | Loci                                                |
| ------------------------------------------- | ------------- | --------------------------------------------------- |
| [{pair.hairpin}](../hairpin/{pair.hairpin}) | {pair.sym_sp} | {pair.loci}:{pair.start}..{pair.end}({pair.strand}) |
| ...                                         | ...           | ...                                                 |
​
​
​
## Target Gene
​
| ID                                       | Species                                | Gene                                                   | Position          |
| ---------------------------------------- | ------------------------------------- | ------------------------------------------------------ | ----------------- |
| [CSMT{target.id}](../target/{target.id}) | {target.coral_sp} \[ {target.sym_sp} ] | [{target.gene}](../gene/{base64_encoded(target.gene)}) | {target.Position} |
| ...                                      | ...                                   | ...                                                    | ...               |

• star

# {info.name}
​
- **ID:** CSMIR{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

# CSMT {target.id}
#### Species
{target.coral_sp} [ {target.sym_sp} ]
​
#### 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.struct)** | {target.LenR} | {target.Rstart} | {target.Rend} | {AlignR} |

Gene

# {gene.name}
​
- **Species:** {gene.species}
- **ID:** CSG/T{gene.id}
​
<a href="/gene/{base64_encoded(target.gene)" class="button">Search in CoralGene</a>
​
<!--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} | [CSMT{target.id}](../target/{target.id}) |
| ...                                        | ...               | ...               | ...                | ...                                     |