February 6, 2017

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

July 4, 2016

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.
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

June 21, 2016

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

September 14, 2015

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

September 11, 2015

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

July 30, 2015

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

April 6, 2015

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

December 12, 2014

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

August 11, 2014

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.

August 1, 2014

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

June 16, 2014

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.

April 29, 2014

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.

March 6, 2014

Tutorial movie in English

The TOGO project has also made a tutorial movie in English. I really appreciate their quick work.

January 9, 2014

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.