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.

aLeaves Introduction on Scribd (in Japanese)

I have uploaded a draft of the article introducing aLeaves in Japanese onto Scribd.

This article will be a part of the next issue of the newsletter of Japanese Society of Evolutionary Studies.

aLeaves in Slideshare

I have uploaded a slide file introducing aLeaves for a presentation I gave last week (in Japanese), onto Slideshare.

I am sorry that most slides are in Japanese. I will make an English version for another talk in the future. I hope Japanese users of aLeaves can get some information about the concept of aLeaves development and how it works.

Brief introduction of aLeaves (mainly in Japanese) from cdb_gras

The first ctenophoran species in the next update

I have just found a set of predicted protein-coding genes for the Mnemiopsis leidyi, a comb jellyfish, at the web site of NHGRI.

This resource will be integrated in the database #12 in the next update of aLeaves, some time late this fall.

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.

Update of aLeaves database

I plan to update the aLeaves sequence databases by the end of this week.

With this scheduled update, the taxonomic coverage at aLeaves will adhere to that of Ensembl release 72 (for vertebrates) and Ensembl Metazoa release 19 (for invertebrates).

I will announce the date and time of the update at the aLeaves main web site.

aLeaves paper now available

An article introducing aLeaves and its link with the MAFFT server has been made available online just a few days ago.


This article will be a part of the Web Server Issue 2013 of Nucleic Acids Research.

Citation details:
aLeaves facilitates on-demand exploration of metazoan gene family trees on MAFFT sequence alignment server with enhanced interactivity
Shigehiro Kuraku, Christian M. Zmasek, Osamu Nishimura and Kazutaka Katoh
Nucleic Acids Research. Web Server Issue 2013, in press.

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.

Database update scheduled today

The databases available at aLeaves will be replaced today to cover more species and sequences, I am sorry if you have some inconvenience because of this.

I will announce again when done.

An update of databases scheduled in mid Feb

I plan to update some aLeaves databases in mid February. The change will include the adoption of the latest Ensembl release.

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).

Beginning this blog site

This blog site has been initiated to announce changes in the aLeaves web server.