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

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

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 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

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.

Update & Best wishes for 2014 !

The aLeaves databases have been updated. As always, they includes the latest sequence sets at NCBI Protein for the covered taxa and the latest release by Ensembl and EnsemblMetazoa. This update newly includes 9 species below. Original data sources are linked from the species' names.


Database #3 (Non-human eutherians)

 Ovis aries (sheep)


Database #4 (Non-mammalian vertebrates)

  Chelonia mydas (green sea turtle)

  Chrysemys picta (painted turtle)


Database #5 (Actinopterygian fish)

  Astyanax mexicanum (Mexican cavefish)

  Lepisosteus oculatus (Spotted gar)


Database #6 (Cartilaginous fishes and cyclostomes)

  Lethenteron japonicum (or L. camtschaticum?; Japanese lamprey)


Database #9 (Arthropods)

  Dendroctonus ponderosae (mountain pine beetle)

  Solenopsis invicta (red fire ant)


Database #12 (Non-bilaterian metazoans)

  Mnemiopsis leidyi (comb jellyfish)


From now on, aLeaves runs 'blastp' of BLAST+ instead of 'blastall' of the 'legacy BLAST'.

Plus, this upgrade includes the change of the timing with which users are guided from the aLeaves server to the MAFFT server, after the search. In brief, the setting page for subsequent clustering process was previously still in the aLeaves server, but now is in the MAFFT server. Thus, users are warned about this in the first page of aLeaves execution.

Update completed with some new species

To adhere to the latest taxonomic coverage of Ensembl and Ensembl Metazoa, the databases for aLeaves have been updated. The below species have been newly included :

Arthropods
Strigamia maritima
Tetranychus urticae
Megaselia scalaris
Rhodnius prolixus
Anopheles darlingi
 
Nematodes
Pristionchus pacificus
Loa loa
Caenorhabditis japonica
Caenorhabditis brenneri
Caenorhabditis remanei

At the same time, new sequences at NCBI Protein (based on submissions of individual researchers) have also been incorporated into the database 7 and 13.

For some species indicated with '#' in the Species page, the peptide sequence sets are available now at Ensembl or Ensembl Metazoa, although they were available only in other site, such as NCBI Protein. We have newly adopted those new resources at Ensembl or Ensembl Metazoa, but also have basically kept the sequence sets that aLeaves has adopted so far.

Plus, I have included the protein-coding gene set of the sea lamprey (Petromyzon marinus) predicted by the genome annotation consortium (Smith et al., 2013. Nat. Genet.) in the database 6 (for 'Cartilaginous fishes and cyclostomes'), because the gene set available at Ensembl (which aLeaves has adopted so far) is quite different from the consortium dataset and may not be comprehensive enough.

Updated !

Details of the update are as follows:

New Ensembl release 70 and EnsemblGenomes Metazoa release 17

Data sets derived from 'Ensembl' and 'EnsemblGenomes Metazoa' have been updated to adhere the latest releases.


New species

Pacific oyster (Crassostrea gigas)

wasp (Nasonia vitripennis)

Southern platyfish (Xiphophorus maculatus) according to Ensembl release 69 and later

Ferret (Mustela putorius furo) according to Ensembl release 69 and later


Altered partitioning between Database 5 & 6

Previously, sequences of the sea lamprey (Petromyzon marinus) were included in Database 5 together with other vertebrates available at Ensembl, while Database 6 has only a single cartilaginous fish, Callorhinchus milii. In the latest setting, sea lamprey sequences are included in Database 6, labelled 'Non-osteichthyan vertebrates'.


'Category ID'

Previously, only sequences from genome-wide resources (also human RefSeq data set) had Species ID (e.g., 'HOMSA' for human) which is recognized at  data set refinement steps the MAFFT server.

To give visual cues for sequences derived from NCBI Protein (Database 7 and 13), I have introduced 'Category ID', which is explained in the table in the 'Species' page .


Additional notes

In parallel with the improvement of the aLeaves server, the interactivity of the MAFFT server is also being improved, in order to better process data sets forwarded from the aLeaves server. Please also try the improved work flow between the two servers by clicking on the link under 'Proceed to tree building' in aLeaves results page.

Digest of updates in the first phase

December 25, 2012 - Two lophotrochozoans (Capitella teleta and Helobdella robusta) were added to the Database #11, following publication of the study involving resources of these genomes (Simakov et al., 2013. Nature).

December 11, 2012 - New function to pass the output to a clustering tool (powered by the MAFFT server) added (still tentative version).

December 7-8, 2012 - Server shutdown because of annual scheduled energy shutdown of RIKEN CDB. 

December 4, 2012 -  Release of non-restricted version.

November 19, 2012 -  Release of beta version (restricted with password).