{APPRIS} issues

Unfortunately, we have identified issues with files from a small number of APPRIS datasets. In each affected dataset, the relevant files have been deleted and a README file has been added to explain the changes. The issues affecting these datasets are outlined below.

Please contact us if you are affected by the issues with these files or their deletion, or you are interested in obtaining updated APPRIS predictions for any of these datasets. As always, we recommend using the most up-to-date APPRIS predictions that are available for a given species.

2019_09.v29/danio_rerio/e98v29

In this dataset, there are two copies of each 'appris_method' file, and the older copy of each file is empty. The older version of each 'appris_method' file has been deleted, leaving the newer version intact. A new bigBed file has been generated for each BED12 file.

2018_12.v28/homo_sapiens/e94v28

In this dataset, the 'appris_method' files have been deleted due to invalid/duplicated records.

2018_12.v28/mus_musculus/e94v28

The 'appris_method' files have been deleted from this dataset due to invalid/duplicated records.

2018_12.v28/homo_sapiens/rs109v28

The 'appris_data' files have been deleted from this dataset due to duplicated records.

2018_07.v27/gallus_gallus/e93

All files have been deleted from this dataset. The 'appris_data' files contained duplicated records, and the 'appris_method' files lacked data for the Z and W sex chromosomes.

2017_06.v23/homo_sapiens/e88v22

A small number of extraneous files have been removed from this dataset.

2017_06.v23/homo_sapiens/rs107v22

A small number of extraneous files have been removed from this dataset.

2017_06.v23/mus_musculus/up201610v23

The file 'appris_data.appris_label.txt' has been removed from this dataset due to apparent file corruption.

{APPRIS} release 2017_08.v24 is out!

We are pleased to announce the launch of the last annotations: http://appris-tools.org

• New APPRIS domain: http://appris-tools.org

The old domains of APPRIS (database, server, and web services) still maintained.

• New release of Ensembl (e90) for the local species.

• Human
• Mouse
• Zebra-fish
• Pig             (new assembly Sscrofa11.1)

• APPRIS-CODE

• APPRIS
• Now the decision of which Matador3D to use is automatic.
• By default, we use Matador3D2 but If we have genome coordinates, then we use Matador3D.
• Bug fixed: although the variant has start/stop codon not found, the correct score of CORSAIR will be printed.
• But the final annotation of APPRIS will be the same. 

• SPADE
• New database with the curated domains of Pfam-A (pfam_201706)

New APPRIS domain

We are pleased to announce the launch of the new domain for APPRIS:
http://appris-tools.org

Don't worry. The old domains of APPRIS (database, server, and web services) still maintained.

APPRIS team

{APPRIS} release 2017_06.v23 is out!

We are pleased to announce the launch of the last annotations: http://appris.bioinfo.cnio.es/

• New release of Ensembl (e88) for the local species.

• New APPRIS annotations using the gene dataset of RefSeq:
• Human       (versions: 108, 107, and 105)
• Mouse        (versions: 106)
• Zebra-fish  (versions: 105)
• Rat             (versions: 106)
• Pig             (versions: 105)
• Chimp        (versions: 104)

• New APPRIS annotations using the UniProt proteome from the gene names:
• Human       (versions: 2017_03, 2016_06)
• Mouse        (versions: 2016_10)
• Zebra-fish  (versions: 2016_10)
• Rat             (versions: 2016_10)
• Pig             (versions: 2017_02)
• Chimp        (versions: 2017_02)

• APPRIS-SERVER
• Bug fixed printing the number of peptides.
• Bug fixed: printing the TMH
• Bug fixed: printing the pop-up annotations of Sequence Browser when the transcript id is too long.
• Print the Matador3D and Matador3D2 residues when the  data-set comes from Ensembl and UniProt/APPRIS, respectively.

• APPRIS-CODE
• Bugs fixed: parsing the SPADE outputs to be saved in the APPRIS databases.
• Matador3D2: updated PDB database (PDB_70_with_pdb_seq).
• Matador3D2 is used in the final decision of APPRIS when the gene set comes from UniProt. Matador3D is used for the rest of the gene sets (Ensembl and RefSeq).
• Bug fixed: getting on consensus section in the THUMP method.

{APPRIS} release 2017_01.v20 is out!

We are pleased to announce the launch of the last annotations: http://appris.bioinfo.cnio.es/

• New release of Ensembl (e87) for all species.
• New annotations for RefSeq human gene data-set (versions 105 and 107 for the assemblies GRCh37 and GRCh38, respectively).
• APPRIS annotations for UniProt human, mouse, zebra-fish, and rat. Proteome versions:
  Human (2016_06)
  Mouse (2016_10)
  Zebra-fish (2016_10)
  Rat (2016_10)

• APPRIS-SERVER:
• Include Advanced Search panel.
• CNIO proteomic evidences (PROTEO) have been included into the SequenceBrowser

• APPRIS-CODE:
• APPRIS:
• Changes in the weight of CORSAIR.
• Changes in the weight of firestar.
• Matador3D v2: Has been included in APPRIS code.
• CORSAIR:
• A variant with "start/stop codons not found" can not to win.

{APPRIS} release 2016_06.v17 is out!

We are pleased to announce the launch of the last annotations: http://appris.bioinfo.cnio.es/

• Principal Isoforms for RefSeq human gene data-set. We have used the versions 105 and 107 for the assemblies GRCh37 and GRCh38, respectively.

• APPRIS-SERVER:
• Changes in the web services, they accept multiple datasets sources (ensembl, refseq)
• Now the search web services retrieves the results for a specific query.
• Add TSL annots in the report web page

• APPRIS-CODE:
• The file names of method results have changed.
• Add TSL and TAG features in "entity" table.
• Change the "namespace" of "datasource" table.
• Delete HAVANA datasource
• APPRIS
• Fixed bug. No decision when the sequence length is equal, with the same appris score.
• Unique "server.json" config file for server.
• Script "appristools_srv" to update the APPRIS release

{APPRIS} release 2016_03.v15 is out!

We are pleased to announce the launch of the last annotations: http://appris.bioinfo.cnio.es/

• Hand-over for Ensembl 84. New gene data-set for Mouse (GENCODE M9) and Zebra-fish. The same for the rest of species:  human, rat, pig, chimp, fruitfly, and C.elegans.
• APPRIS is a public trackHub in UCSC: https://genome.ucsc.edu/cgi-bin/hgHubConnect 

• Creation of SPADE2. New algorithm for the detection of whole protein domains based on the bit-score of Pfam alignment.
• Improvements in the Matador3D method.