Cephalopod Genome Browser

CephRes-gdatabase (CephRes Genomes Database) is an open genomic resource aimed to support cephalopod biologists and all evolutionary and comparative genome biologists to explore genomic data of these fascinating organisms. It represents a resource for mining various genomes of octopuses and other cephalopod species to help advancing cephalopod genomics and to discover their genomic novelties. Through the use of the browsers it is possible to visualize whole genomes on different scales, until single base pair resolution.

The graphical interfaces which visualize the different genome assemblies is based on the genome browser originally designed by Kent and coworkers (2002; Genome Res. 12: 996-). Currently, the genomes of two Octopus species (O. bimaculoides and O. vulgaris) and the one of another octopus, Callistoctopus minor, and of the Hawaiian bobtail squid (Euprymna scolopes) can be accessed below. Next implementations will include other cephalopod species.

How the database works
CephRes-gdatabase is made by a “genome browser” based on Kent et al. (2002) including some tools such as the table browser, BLAT and custom tracks. The features available allow also to connect with other databases such as Ensembl, Primer3Plus, etc.
This genome database browsing and mining initiative is a joint venture of CephRes and UniVienna.

Features implemented
Table browser:
The table browser enables the user to mine and filter big datasets using several parameters which produces subsets that can be compared.

BLAT:
This Blast-Like-Alignment tool allows for fast alignments of any sequence with a minimum length of at least 25 bp.
Tools –Blat
Enter your query as a nucleotide or protein sequence
Output: List of best matches to your query.
Details: nucleotide sequence;scaffold id,matching regions;….
Browser: graphical view of your alignment on the genome

Custom tracks
It is possible to upload your private data to the genome browser:
My data – Custom tracks – Paste URLs or data:
Enter the gene position: ScaffoldID_StartPos_StopPos_GeneID
or
Enter the gene sequence
My data – Custom tracks – Optional track documentation:
Enter your personal gene annotation.
More information on how to add custom tracks can be find here:
https://genome-euro.ucsc.edu/goldenPath/help/customTrack.html

In silico PCR
By entering possible primers it is possible to simulate a PCR in silico against the entire genome, which will permit more efficient and specific primer design.

Sessions tool
By creating a session you can save the current mode of the genome browser and go back to the same settings at a later time.
For more info see:
http://metazoa.csb.univie.ac.at/ugb/public/goldenPath/help/hgSessionHelp.html

Octopus vulgaris

The reference guided genome assembly of O. vulgaris described in Zarrella et al. (under revision) can be accessed here. For a more detailed description of the different assembly characteristics please refer to Zarrella et al. Annotation tracks are absent in the genome browser due to the short scaffold length which impedes gene prediction.

Information on the biology of the common octopus (O. vulgaris) and its description is available through various sources. A short overview will be provided here in the next future.

Octopus bimaculoides

The genome browser of O. bimaculoides includes the data published by Albertin et al., 2015. Gene prediction models are added in the genome browser.
Information on the biology of the California two-spot octopus (O. bimaculoides) and its description is available through various sources. A short overview will be provided here in the next future.

Callistoctopus minor

The genome browser of C. minor includes the data published by Kim et al., 2018. Information on the biology of the Korean common octopus (C. minor) and its description is available through various sources. A short overview will be provided here in the next future

Euprymna scolopes

The genome browser of E. scolopes includes the data published by Belcaid et al., 2019. Gene prediction models are added in the genome browser.

For this species we also provide access to: Peptide sequences; (CoDing) CDS sequences; Gene locations.
Information on the biology of the Hawaiian bobtail squid (E. scolopes) and its description is available through various sources. A short overview will be provided here in the next future.