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.

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