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.

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.