Database Update Completed

Despite my expectation included at the end of my previous database update notification, many of us are still in the midst of lasting anxiety caused by the COVID19 pandemic, I guess. To be honest, I did not imagine that it would last so long.

In this update, the database has adopted Ensembl release 104 and Ensembl Genome release 51. The subset of the database derived from NCBI has also been updated.

In total, 39 species based on recently released genome sequences have been newly covered, which are marked with '*' in the Species page.  

I mostly enjoy adding new species to this page (based largely on manual steps) and memorizing their names, while it can be a pain if I have little time for the work. The species that attracted me the most in the today's work was this species - superb fairywren (ルリオーストラリアムシクイ), which lives in Eastern Australia and is famous for sexual dimorphism.

Because of my new appointment at National Institute of Genetics in Mishima, I need to make some decisions about the continuation of this and other web servers. Still, nothing will change for an upcoming year, I believe.

Shigehiro Kuraku

Database update

Please be notified about the work ongoing for updating the aLeaves database. This work will take a few upcoming hours.

Shigehiro Kuraku

Update in April 2020, in the midst of the COVID-19 threat

After a very long interval (ca.2 years), I have updated the sequence database for aLeaves. This update does not only incorporate an increment in NCBI but also encompasses some of the species in Ensembl and Ensembl Metazoa introduced after the last update in 2018 (Ensembl release 93 and Ensembl Metazoa release 38). In total, 10 sauropsids (reptiles and birds), 6 actinopterygian fishes, and 1 invertebrate deuterostome have been newly included (marked with '*' in this Species page) which are listed below:

Sauropsids
Dromaius novaehollandiae (emu)  
Struthio camelus australis (African ostrich)   
Strigops habroptila  (owl parrot or kakapo) 
Crocodylus porosus (Australian saltwater crocodile)
Pogona vitticeps (central bearded dragon)
Notechis scutatus (Mainland tiger snake)
Chelonoidis abingdonii (Abingdon island giant tortoise)
Sphenodon punctatus (tuatara)   
Salvator merianae (Argentine black and white tegu)    
Gopherus agassizii (Agassiz’s desert tortoise)

Actinopterygian fishes
Esox lucius (northern pike)
Ictalurus punctatus (channel catfish)   
Hippocampus comes (tiger tail seahorse)   
Mola mola (ocean sunfish)   
Paramormyrops kingsleyae (elephant fish or elephant nose fish)   
Scleropages formosus (Asian arowana)

Invertebrate deuterostome
Branchiostoma lanceolatum (European lancelet or Mediterranean amphioxus)

More species (especially, mammals and actinopterygian fishes) have been covered by Ensembl, but I have adopted only the species above, to minimize the manual and computational load of maintenance while maximizing the species diversity.

I truly hope that we will be in a more comfortable world when I commit the next update.

Stay safe and healthy,

Shigehiro Kuraku

Update the database to include approx. 40 species

More than a year after the last update, I have updated all the databases to incorporate Ensembl release 93 and gene models of quite a few species with emerging genome-wide sequence data. The species newly introduced have been marked with a red asterisk ('*') in the species list in this page.

Particularly, I am delighted to announce that they now include three elasmobranch shark species, brownbanded bamboo shark, cloudy catshark, and whale shark, whose genome assemblies and gene models were produced in my lab in Kobe (see our original paper published online today in Nature Ecology and Evolution).

I have also included gene models of the Madagascar ground gecko Paroedura picta for which my lab performed de novo genome sequecing and gene prediction (see our original paper published earlier this year in BMC Biology).

Shigehiro Kuraku

Our original Arctic lamprey gene model included

We have performed gene model inference on the publicly available Arctic lamprey (Lethenteron camtschaticum) genome assembly LetJap1.0 released by the group of Dr. Byrappa Venkatesh and have included the resultant predicted peptides in the Database #6 at aLeaves.

The detailed procedure of this gene model inference will be introduced in one of our upcoming publications now under revision. The GFF3 file from which the predicted peptides was derived is also available at our laboratory web site for your use in RNA-seq, ChIP-seq, ATAC-seq read mapping, etc.

S. Kuraku

Databases updated to include 10 more invertebrate species

With one week delay, I have updated all the databases for searches at aLeaves. This reflects inclusion of new species at EnsemblMetazoa release 31 listed below.

• Belgica antarctica (Antarctic midge)
• Bombus impatiens (common bumblebee)
• Lepeophtheirus salmonis (salmon louse)
• Lingula anatina (a brachiopod)
• Lucilia cuprina (Australian sheep blowfly)
• Octopus bimaculoides (California two-spot octopus)
• Sarcoptes scabiei (itch mite): gene set SscaA1.1 from VectorBase
• Stegodyphus mimosarum (African social velvet spider)
• Strongyloides ratti (parasitic nematode): from WormBase WS250
• Thelohanellus kitauei (a myxosporean)

To see where these individual species are categorized, please refer to the Species page (marked with '*') at the server.

Please feel free to contact me if you have any question, bug report, or request of adding more species.

S. Kuraku

aLeaves Databases Update Scheduled

Let me announce to you that I plan to update the aLeaves databases next Monday on the 27th - it has been more than a year since the last update.

This time, ten invertebrate species new to Ensembl Metazoa will be added to the aLeaves species list. In addition, as usual, gene sets for some species will be revised, thanks to new Ensembl gene build, and new sequences in NCBI GenPept will be included in the database 7 and 13.

Shigehiro Kuraku

aLeaves back in full service

The problem reported here last Friday has been fixed, and aLeaves is now working well. I am planning a database update within this year.

S. Kuraku

Link to the MAFFT server is disabled now

Currently, aLeaves works, but its search results cannot be passed to the MAFFT web server. It will take some time to fix it, and please be patient.

S. Kuraku

Searches at aLeaves accelerated

I hope there was no trouble on the users's side caused by the replacement of the web server done the day before yesterday. Because of enhanced capacity of the server machine and modification of aLeaves scripts, searches are now processed much faster, say, by hundreds times.

As a result of this change, after a search job is submitted to aLeaves, you will see the page saying 'Search started !' after a bit longer moment than before and will be directly taken to the search result page.

I hope this change will help you a lot.

S. Kuraku

aLeaves Databases Updated

I have updated the all databases for aLeaves. Now Ensembl release 79 and Ensembl Genome Metazoa release 26 have been adopted.

In this update, we have two new species for Arthropoda:

Melitaea cinxia (Glanville fritillary)
Zootermopsis nevadensis (termite)

 I was wondering what to do with the dozens of bird genomes, but for this update, I have decided not to include them.

S. Kuraku

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.