Web interface

Web Access
Searching for exisiting datasets
Creating new databases

Web Access

The webinterface is available at: bcdatabaser.molecular.eco

Searching for exisiting datasets

You might find already created databases for your given research question. The search interface on the left hand side allows a quick scan for previous requests, alongside statistical information.

Searching

This is possible without logging in with an ORCID.

Creating new databases

ORCID

The web interface requires authentification using an ORCID to associate your requests and final datasets with your account.

Parameters

Most of the parameters are set to a default in the web-interface. If you need more flexibility, please check the command line version.

Fixed parameters:

--check-tax-names If your taxa restriction file contains taxa not supported in the NCBI taxonomy, the tool is unable to search for sequences of this taxon. The web interface automatically halts in this situation, so that you are aware of this situation.
--sequences-per-taxon=9 Several taxa, e.g. model taxa, often have several hundreds of sequences deposited, which usually do not carry new information and are redundant. This parameter will select only the 9 longest sequences available, given below length restriction.
--sequence-length-filter=100:2000 Most barcoding studies use small or average read length, given technological restrictions (e.g. Sanger, Illumina). With this range this we exclude longer sequences, as e.g. whole genome sequences that could cause trouble by false random assignments.

Required parameters:

Search String: This string searches for the marker of interest. You can search for multiple arguments using "OR", be aware though that the first argument will determine the output name. e.g. COI OR CO1 OR 'Cytochrome oxidase 1' OR 'Cytochrome oxidase I'

Optional parameters:

Taxonomic Range: Only child taxa of this will be considered (case sensitive), e.g. Viridiplantae or Brassica
Taxa List: You can supply a file list with taxa names, with each line a new taxon. The sequence selection will be restricted to these groups. This can contain species names, or also higher taxonomic ranks, e.g.
```
Brassica napus
Bellis
Poaceae
```

Request queue

Requests are handled in order of their submission, meaning that your job may start immediately or delayed. You can check the status at the bottom of the page

queue

the job was successfully finished, you can find the results on the right side added to previous results.

this job is currently worked on

this job is waiting for other jobs to be completed before it is started

this job failed. It may be due to several reasons, connection issues or taxa were not found. Pleas check the Details page and feel free to open an issue in case you can not interpret the error.

Download

You will find the download, DOI and citation information with your name as database author on Zenodo

Zenodo