Archive by Author | Andrea Telatin

FTP area updated

Misc-Download-iconWe updated our FTP area, now including datasets from other Nannochloropsis species and strains and the list of families of orthologous proteins obtained from the comparison of N. gaditana and N. oceeanica predicted proteins.

Families of orthologous proteins: file type

venn_protein_clusters
Comparing the protein families of N. gaditana and N. oceanica, we produced the lists of exclusive proteins of each species. These lists are available for download in our FTP area.
Each file is a list of families of orthologous proteins. All the families of each file are populated only by proteins belonging to one species of Nannochloropsis. The families may contain proteins of one or more strains of the same Nannochloropsis species.
In the .txt files there is one family per line, described by the name of the organism (species and strain), then a “|”, the list of the proteins of that organism (indicated by the protein ID) the name of the following organism, another “|”, the proteins of the following organism and finally the annotation of the listed proteins.
 
example:
N.gaditanaB-31|Naga_100019g47.1 N.gaditanaCCMP526|Nga20827 nudix hydrolase;

Even though the differences and the imprecisions of the various gene predictions probably play a major role in the determination of the differences among the two species, a close look at the lists of proteins that are putatively assigned as characteristic of each species my reserve interesting surprises!

References

  1. Corteggiani Carpinelli, E. et al. “Chromosome scale genome assembly and transcriptome profiling of Nannochloropsis gaditana in nitrogen depletion.Molecular Plant (2014) 7 (2): 323-335.doi: 10.1093/mp/sst120

Thank you!

We currently have more than 1.000 unique visitors per month, accounting for roughly 18,000 pageviews per month. Visitors are spread across the four continents…  Thank you for keeping alive Nannochloropsis.org. We are doing our best to update this site and we are also preparing new resources (to be released soon).

This week’s visits

 

Annotation file available

Upon user request we uploaded the GFF version of Nannochloropsis gaditana annotation. This file is in standard GFF3 format, and features refers to the assembled genome (i.e. scaffolds).

You can download the file from the Nannochloropsis genome FTP area.

Paper online

Our paper “Chromosome scale genome assembly and transcriptome profiling of Nannochloropsis gaditana in nitrogen depletion” is online.
You can access it from the Publisher’s website.

Open day

When first published, nannochloropsis.org, has been a private website providing access only upon request. We are glad to offer online the first release of the genome portal! Stay tuned (more features are coming 🙂

MetaCyc database uploaded

In the download area of the website a link for the MetaCyc database is now available.

MetaCyc is a comprehensive tool for metabolic pathways description and analysis. The database is a collection of annotation and sequence files in the proper format for the MetaCyc desktop app to work. Beside this we  set up a web based version of the database, to allow the browsing of metabolic pathways without the need for the complete MetaCyc package to be installed locally.