Scheduled shutdown of aLeaves Server

The aLeaves Server will be shutdown for a few hours starting at 10am (Japanese time) next Monday (December 15th).

S. Kuraku

aLeaves databases based on Ensembl 76

It took more than half a year since the last update. At aLeaves, now you have access to a new set of databases including latest sequences from Ensembl release 76 announced just last week. The species newly included as a result of this update are below:

Papio anubis (Olive baboon) in Database 3 (non-human eutherians)

Alligator sinensis (Chinese alligator) & Poecilia formosa (Amazon molly) in Database 5 (non-mammalian vertebrates)

Onchocerca volvulus in Database 10 (nematodes)

I know that there are many more metazoan speices whose genome sequencing has been conducted, than covered at aLeaves, but basically I include only species whose predicted peptide sequences are available somewhere online, and if not in Ensembl, the products from the genome project should already be published. Still, my knowledge is not enough, so please let me know if you know any speices that fits this criteria.

Next update soon

I will include the sequences from the next Ensembl release (76) in the next update of aLeaves databases.

Previously, I announced that I would update them by the end of July, but please wait for a while for the Ensembl release 76 to be out.

S. Kuraku

Elephant shark peptides replaced

In a different line of research, I realized the other day that peptides for Callorhinchus milii (elephant shark) retrieved from NCBI and included in the Database 6 for aLeaves are derived from transcripts, but not from the genome.

Thus, I have downloaded the file 'Predicted proteins' in the project web site and have replaced those in Database 6 with the newly downloaded peptides predicted on the genome assembly. I am sorry for any misidentification or confusion about this.

All the databases have not been updated for about half a year. Although there seems to be little addition, according at least to the announcement from Ensembl, I plan to commit an update by the end of July. Please be patient.

Brief introduction of aLeaves

I have uploaded a slide file briefly introducing aLeaves on SlideShare. The slides were made for an a closed tutorial event 'Sequence Informatics Afternoon' organized for researchers in CDB by my lab in Kobe.

Brief introduction of aLeaves from cdb_gras

Tutorial movie in English

The TOGO project has also made a tutorial movie in English. I really appreciate their quick work.

aLeaves tutorial movie in Japanese

A tutorial movie showing how to use aLeaves has been newly made by TOGO Database Project run by Database Center for Life Science in Japan.

A minor update - whole elephant shark genome

I have replaced the set of elephant shark peptides with the one based on the whole genome assembly recently published by the group in Singapore (Venkatesh et al., 2014).

The species ID has not changed ('CALMI').

This is the only representative of the group Chondrichthyes (cartilaginous fish) at the moment.