appris-announce Mailing List for APPRIS
A system for annotating alternative splice isoforms
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appris-announce — A low volume mailing list used to announce major updates and major releases.
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From: José M. R. <jmr...@cn...> - 2014-08-11 10:21:52
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Dear all, APPRIS release 3.4.1 is out for Gencode20 and GencodeM3 http://appris.bioinfo.cnio.es/ The new list of principal isoforms still is: Gencode20 http://appris.bioinfo.cnio.es/download/data/homo_sapiens/appris_data.principal.txt GencodeM3 http://appris.bioinfo.cnio.es/download/data/mus_musculus/appris_data.principal.txt The archived files are: Gencode19 http://appris.bioinfo.cnio.es/download/data/gencode19/appris_data.principal.txt GencodeM2 http://appris.bioinfo.cnio.es/download/data/gencodeM2/appris_data.principal.txt Highlights of this release include: * APPRIS-DATA - Human > Gencode 20 (GRCh38) - Mouse > Gencode M3 (GRCm38) * APPRIS-WEBSITE - CExonic is DEPRECATED - Add PROTEO annotations - Improve Web Site features. - Include PROTEO RESTful service into web site. Best Regards, J ********************************************* To post a message to all the list members, send email to app...@li... To subscribe/unsubscribe, https://lists.sourceforge.net/lists/listinfo/appris-announce For the latest news visit our blog, http://sourceforge.net/p/appris/blog **NOTA DE CONFIDENCIALIDAD** Este correo electrÿnico, y en su caso los ficheros adjuntos, pueden contener informaciÿn protegida para el uso exclusivo de su destinatario. Se prohÿbe la distribuciÿn, reproducciÿn o cualquier otro tipo de transmisiÿn por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido. **CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. Distribution, reproduction or any other use of this transmission by any party other than the intended recipient is prohibited. If you are not the intended recipient please contact the sender and delete all copies. |
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From: José M. R. <jmr...@cn...> - 2013-12-20 10:18:27
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Dear all, APPRIS release 3.2.3 is out! Highlights of this release include: - New release of annotations of Gencode19. Genes have external name. Happy Holidays and Happy New Year, J ********************************************* To post a message to all the list members, send email to app...@li... To subscribe/unsubscribe, https://lists.sourceforge.net/lists/listinfo/appris-announce For the latest news visit our blog, http://sourceforge.net/p/appris/blog **NOTA DE CONFIDENCIALIDAD** Este correo electrÿnico, y en su caso los ficheros adjuntos, pueden contener informaciÿn protegida para el uso exclusivo de su destinatario. Se prohÿbe la distribuciÿn, reproducciÿn o cualquier otro tipo de transmisiÿn por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido. **CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. Distribution, reproduction or any other use of this transmission by any party other than the intended recipient is prohibited. If you are not the intended recipient please contact the sender and delete all copies. |
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From: José M. R. <jmr...@cn...> - 2013-12-12 09:53:40
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Dear all, APPRIS release 3.2.2 is out! Highlights of this release include: - Human > Update annotations for Gencode 19 (Ensembl 74) - Mouse > Update annotations for Gencode M2 (Ensembl 74) - Rat > Update annotations for Ensembl 70 - Zebrafish > Update annotations for Ensembl 70 A complete list of the changes can be found at https://sourceforge.net/p/appris/code/HEAD/tree/trunk/CHANGE.log Best Regards, J ********************************************* To post a message to all the list members, send email to app...@li... To subscribe/unsubscribe, https://lists.sourceforge.net/lists/listinfo/appris-announce For the latest news visit our blog, http://sourceforge.net/p/appris/blog **NOTA DE CONFIDENCIALIDAD** Este correo electrÿnico, y en su caso los ficheros adjuntos, pueden contener informaciÿn protegida para el uso exclusivo de su destinatario. Se prohÿbe la distribuciÿn, reproducciÿn o cualquier otro tipo de transmisiÿn por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido. **CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. Distribution, reproduction or any other use of this transmission by any party other than the intended recipient is prohibited. If you are not the intended recipient please contact the sender and delete all copies. |
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From: José M. R. <jmr...@cn...> - 2013-08-16 11:33:36
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Dear all, APPRIS release 3.1.1 is out! Most of the changes are within "WebSite". The Highlights of this release include: - Links of archives redirect to more specific website. - Rename the suffix of data files of 'rattus_norvegicus'. - Change the annotations of SPADE and THUMP. Now, we print their "scores" in the website: - SPADE shows an float number where the absolute number is the pfam domains that are detected. Then, the number after the decimal indicates the numbers of partial domains. - THUMP shows the number of TMH detected. Again, the number after the decimal indicates the partial TMH. - Delete the phrase "on Human (GRCh37/hg19) Assembly" from the 'report' web page. - Fix the URL that retrieves proteomics data as BED format. - Update the proteomic data (gencode12): - Peptides were assembled from five previously available proteomics data sets. Three of the peptide data sets came from published large-scale experiments (Ezkurdia, Nagaraj, Geiger) and the others were from two large spectra libraries, PeptideAtlas (Farrah) and NIST (http://peptide.nist.gov/). These tracks show where peptide evidence exists (0 or 1) , but there is no means of scoring these tracks. ********************************************* To post a message to all the list members, send email to app...@li... To subscribe/unsubscribe, https://lists.sourceforge.net/lists/listinfo/appris-announce For the latest news visit our blog, http://sourceforge.net/p/appris/blog **NOTA DE CONFIDENCIALIDAD** Este correo electrÿnico, y en su caso los ficheros adjuntos, pueden contener informaciÿn protegida para el uso exclusivo de su destinatario. Se prohÿbe la distribuciÿn, reproducciÿn o cualquier otro tipo de transmisiÿn por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido. **CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. Distribution, reproduction or any other use of this transmission by any party other than the intended recipient is prohibited. If you are not the intended recipient please contact the sender and delete all copies. |
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From: José M. R. <jmr...@cn...> - 2013-07-26 08:05:24
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Dear Mark, Due to APPRIS accepts genes from other new species (mouse and rat), a few new changes has been made in the website. For example, * Website Links: - Older links: http://appris.bioinfo.cnio.es/report.html?id=ENSG00000012048&namespace=Ensembl_Gene_Id http://appris.bioinfo.cnio.es/report.html?id=ENST00000357654&namespace=Ensembl_Transcript_Id - New links: (Human) http://appris.bioinfo.cnio.es/report.html?id=ENSG00000012048&namespace=Ensembl_Gene_Id&specie=homo_sapiens http://appris.bioinfo.cnio.es/report.html?id=ENST00000357654&namespace=Ensembl_Gene_Id&specie=homo_sapiens (Mouse) http://appris.bioinfo.cnio.es/report.html?id=ENSMUSG00000022721&namespace=Ensembl_Gene_Id&specie=mus_musculus (Rat) http://appris.bioinfo.cnio.es/report.html?id=ENSRNOG00000001885&namespace=Ensembl_Gene_Id&specie=rattus_norvegicus * REST services: Older links (This REST services still working): http://appris.bioinfo.cnio.es/ws/latest/rest/appris/id/ENSG00000099904 New links: (Human) http://appris.bioinfo.cnio.es/ws/rest/appris/id/homo_sapiens/ENSG00000099904 (Mouse) http://appris.bioinfo.cnio.es/ws/rest/matador3d/id/mus_musculus/ENSMUSG00000022721 (Rat) http://appris.bioinfo.cnio.es/ws/rest/matador3d/id/rattus_norvegicus/ENSRNOG00000001885 Sorry for any inconvenience. Best Regards, Jose Rodríguez ********************************************* To post a message to all the list members, send email to app...@li... To subscribe/unsubscribe, https://lists.sourceforge.net/lists/listinfo/appris-announce For the latest news visit our blog, http://sourceforge.net/p/appris/blog Begin forwarded message: >> >> The links in the UCSC genome browser to APPRIS have quit working. Links like: >> >> http://appris.bioinfo.cnio.es/report.html?id=ENSG00000012048&namespace=Ensembl_Gene_Id >> http://appris.bioinfo.cnio.es/report.html?id=ENST00000357654&namespace=Ensembl_Transcript_Id >> >> >> now product: >> >> Your query does not match any genes in the database. Note that the query must: >> >> have alphanumeric values, at least one of which must be a letter >> be at least three characters long >> valid Ensembl identifier. >> For this cases, you have to give the exact identifier. >> >> >> Cheers, >> Mark > **NOTA DE CONFIDENCIALIDAD** Este correo electrÿnico, y en su caso los ficheros adjuntos, pueden contener informaciÿn protegida para el uso exclusivo de su destinatario. Se prohÿbe la distribuciÿn, reproducciÿn o cualquier otro tipo de transmisiÿn por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido. **CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. Distribution, reproduction or any other use of this transmission by any party other than the intended recipient is prohibited. If you are not the intended recipient please contact the sender and delete all copies. |
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From: José M. R. <jmr...@cn...> - 2013-07-25 14:40:06
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Dear all, APPRIS release 3.1 is out! We are pleased to announce that the latest APPRIS update has been released, which can be accessible via the website (http://appris.bioinfo.cnio.es) The Highlights of this release include: * APPRIS-CODE: We have decided to establish new nomenclature of version of appris's code. - v1.1: - SPADE does not migrate domains of variants with the same sequence where pfamscan does not provide results. For example, ENSG00000021300.7 (Gencode 15) - FIRESTAR prints results whose cutoff is smaller than 65%. This is bad!!! For example, ENSG00000184361 (Gencode 15) - CORSAIR, v10. We have added the new scores of the rest of species (including Lynx pardinus): 'Rest of species' 'Homo sapiens' => 1, 'Pan troglodytes' => 1, 'Mus musculus' => 1.1, 'Rattus norvegicus' => 1.1, 'Bos taurus' => 1.2, 'Canis lupus familiaris' => 1.2, 'Sus scrofa' => 1.2, 'Monodelphis domestica' => 1.3, 'Gallus gallus' => 2, 'Taeniopygia guttata' => 2, 'Anolis carolinensis' => 2, 'Xenopus tropicalis' => 2.2, 'Tetraodon nigroviridis' => 2, 'Danio rerio' => 2.5, * APPRIS-DATA: - Human > Gencode 12, rel12.27Jun2013.v5 > Gencode 15, g15.v3.15Jul2013 * NEW GENOMES: - Mouse > Ensembl70, e70.v3.15Jul2013 - Rat > Ensembl70, e70.v3.10Jul2013 * APPRIS-WEBSITE: - Add script for the rest of species - Include new data files into website: - appris data exon by exon - Modify "download" web page. Best Regards, The APPRIS Team ********************************************* To post a message to all the list members, send email to app...@li... To subscribe/unsubscribe, https://lists.sourceforge.net/lists/listinfo/appris-announce For the latest news visit our blog, http://sourceforge.net/p/appris/blog **NOTA DE CONFIDENCIALIDAD** Este correo electrÿnico, y en su caso los ficheros adjuntos, pueden contener informaciÿn protegida para el uso exclusivo de su destinatario. Se prohÿbe la distribuciÿn, reproducciÿn o cualquier otro tipo de transmisiÿn por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido. **CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. Distribution, reproduction or any other use of this transmission by any party other than the intended recipient is prohibited. If you are not the intended recipient please contact the sender and delete all copies. |
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From: jmrodriguez <jmr...@cn...> - 2013-06-11 15:58:55
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Dear all, We are pleased to announce that the latest APPRIS update (a!2) has been released : http://appris.bioinfo.cnio.es/ Highlights of this release include: Human: A new APPRIS release, v2, for Gencode15/Ensembl 70, is available. Mouse: A new APPRIS release, v2, for Ensembl 70, is available... But is not on the website yet. For the latest news from the APPRIS project visit our blog at http://sourceforge.net/p/appris/blog/ Best Regards, Jose Rodríguez. -- ********************************************* Jose Manuel Rodriguez Carrasco e-mail: jmr...@cn... Tlfn: (+34) 91 732 80 00 ext: 3061 Structural Biology and BioComputing Programme Spanish National Cancer Center (CNIO) Spanish National Bioinformatics Institute (INB) - http://www.inab.org - Address: C/ Melchor Fernandez Almagro 3, Madrid (Spain) ZipCode: 28029 **NOTA DE CONFIDENCIALIDAD** Este correo electrónico, y en su caso los ficheros adjuntos, pueden contener información protegida para el uso exclusivo de su destinatario. Se prohíbe la distribución, reproducción o cualquier otro tipo de transmisión por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido. **CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. Distribution, reproduction or any other use of this transmission by any party other than the intended recipient is prohibited. If you are not the intended recipient please contact the sender and delete all copies. |
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From: jmrodriguez <jmr...@cn...> - 2013-06-11 15:52:58
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Test -- ********************************************* Jose Manuel Rodriguez Carrasco e-mail: jmr...@cn... Tlfn: (+34) 91 732 80 00 ext: 3061 Structural Biology and BioComputing Programme Spanish National Cancer Center (CNIO) Spanish National Bioinformatics Institute (INB) - http://www.inab.org - Address: C/ Melchor Fernandez Almagro 3, Madrid (Spain) ZipCode: 28029 **NOTA DE CONFIDENCIALIDAD** Este correo electrónico, y en su caso los ficheros adjuntos, pueden contener información protegida para el uso exclusivo de su destinatario. Se prohíbe la distribución, reproducción o cualquier otro tipo de transmisión por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido. **CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. Distribution, reproduction or any other use of this transmission by any party other than the intended recipient is prohibited. If you are not the intended recipient please contact the sender and delete all copies. |
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From: jmrodriguez <jmr...@cn...> - 2013-06-11 15:47:58
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Test body -- ********************************************* Jose Manuel Rodriguez Carrasco e-mail: jmr...@cn... Tlfn: (+34) 91 732 80 00 ext: 3061 Structural Biology and BioComputing Programme Spanish National Cancer Center (CNIO) Spanish National Bioinformatics Institute (INB) - http://www.inab.org - Address: C/ Melchor Fernandez Almagro 3, Madrid (Spain) ZipCode: 28029 **NOTA DE CONFIDENCIALIDAD** Este correo electrónico, y en su caso los ficheros adjuntos, pueden contener información protegida para el uso exclusivo de su destinatario. Se prohíbe la distribución, reproducción o cualquier otro tipo de transmisión por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido. **CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. Distribution, reproduction or any other use of this transmission by any party other than the intended recipient is prohibited. If you are not the intended recipient please contact the sender and delete all copies. |
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From: Jose M. R. <jo...@gm...> - 2013-06-11 15:34:57
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From: Jose M. R. <jo...@gm...> - 2013-06-11 15:31:50
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