SPANR Splicing-based Analysis of Variants
SPANR addresses a key unmet challenge in genomics research, which is to ascertain how single nucleotide variations (SNVs) cause splicing misregulation and may lead to disease. This tool can analyze synonymous, missense and nonsense exonic SNVs, as well as intronic SNVs that are up to 300nt from splice junctions. Because of limited computational support, we have retired the interactive SPANR web tool and only offer a pre-computed, genome-wide index of splicing variants called SPIDEX from now on.
If you use this tool in research, please cite
Hui Y. Xiong, Babak Alipanahi, Leo J. Lee, Hannes Bretschneider, Daniele Merico, Ryan K.C. Yuen, Yimin Hua, Serge Gueroussov, Hamed S. Najafabadi, Timothy R. Hughes, Quaid Morris, Yoseph Barash, Adrian R. Krainer, Nebojsa Jojic, Stephen W. Scherer, Benjamin J. Blencowe, Brendan J. Frey*,
The human splicing code reveals new insights into the genetic determinants of disease.
Science DOI: 10.1126/science.1254806. Published Online December 18 2014.
User License Agreement
SPIDEX may be freely used for research where all findings are made publicly available. Please read the user license agreement below and fill out the forms to download SPIDEX.
PLEASE READ THIS END USER LICENSE AGREEMENT (“EULA”) CAREFULLY BEFORE USING THE ANNOVAR SPIDEXTM DATABASE (AS DEFINED BELOW). BY USING THE ANNOVAR SPIDEXTM DATABASE YOU CERTIFY THAT YOU ARE AN ACADEMIC OR NOT-FOR-PROFIT END USER (AS DEFINED BELOW) AND YOU AGREE TO BE BOUND BY THE TERMS OF THIS EULA, AS THESE MAY BE UPDATED FROM TIME TO TIME. IF YOU DO NOT AGREE TO THESE TERMS, DO NOT USE THE ANNOVAR SPIDEXTM DATABASE AND WHEN PRESENTED WITH THE OPTION TO “AGREE” OR “DECLINE” THE TERMS OF THIS EULA, CLICK “DECLINE”.
This END USER LICENSE AGREEMENT (“EULA”) for Academic or Not-for-Profit end users (“ANPEU”) is a legally binding contract between you, an ANPEU, and Deep Genomics. In this EULA, an ANPEU means a scientist undertaking research activities in an academic institution, government research laboratory, or not-for-profit organization (“Institution”) where neither the scientist not the Institution is engaged with a commercial entity in any manner, including undertaking research and development on behalf of a commercial organization, related to the subject matter of this EULA. Deep Genomics and you may be individually referred to in this EULA as a “Party” and collectively as “Parties.”
Deep Genomics has developed a proprietary genome-wide database of scores that predict the functional effects of single nucleotide variants (SNVs) on cassette splicing (“SpidexTM Database”). Deep Genomics has made the SpidexTM Database freely available for use by ANPEUs on ANNOVAR (“ANNOVAR SpidexTM Database”) for scientific research purposes only.
THE FOLLOWING TERMS WILL GOVERN YOUR USE OF THE ANNOVAR SPIDEXTM DATABASE.
1. GRANT AND SCOPE OF LICENSE
1.1. Permitted uses. Deep Genomics grants you a non-exclusive, revocable, non-transferable, and limited right to use the ANNOVAR SpidexTM Database for the purpose of undertaking academic, governmental, or non-for-profit research (“Scope of License”).
1.2. Prohibited uses. Your use of the ANNOVAR SpidexTM Database is limited to the Scope of License as described in Section 1.1 above. For clarity, you may not:
a) at any time, directly or indirectly, dispute or contest the exclusive licensing rights of Deep Genomics in SpidexTM Database; transfer or assign any of your rights or obligations under this EULA to any third party without the prior written consent of Deep Genomics; disclose, provide, or to otherwise make SpidexTM Database or access thereto available in full or in part and in any form to any third party or natural or legal person (“Person”);
b) use SpidexTM Database or data generated therefrom for any non-academic purposes or applications of any kind;
c) copy, translate or modify SpidexTM Database and any other copyrighted work or confidential information provided by Deep Genomics in relations to SpidexTM Database or grant third parties access or rights to changed or modified versions of SpidexTM Database;
d) use, advertise, promote, market, or refer to SpidexTM Database in any manner likely to negate, impair, dilute, or adversely affect the reputation of or any of the rights of Deep Genomics as exclusive licensee of SpidexTM Database;
e) reproduce, make, have made, use, import, export, or sell any product or service derived from the use of SpidexTM Database without express written permission from Deep Genomics under separate license;
f) disclose the results of any benchmark tests conducted by you using SpidexTM Database to any third party without the prior written approval of Deep Genomics;
g) in whole or in part, whether modified or unmodified, incorporate SpidexTM Database into other programs or sublicense SpidexTM Database to any third parties;
h) work around, reverse engineer, decompile, disassemble SpidexTM Database, publish for others to copy, rent, lease, lend, or host SpidexTM Database to or for third parties for any reason; and
2. OWNERSHIP
Without prejudice to the permitted uses granted to you in Section 1.1 above, Deep Genomics has the exclusive rights in all copies of SpidexTM Database, including the copy hosted on ANNOVAR, in full or in part, as well as the right to distribute, sub-license, display, and make derivative works of SpidexTM Database, as uploaded into ANNOVAR or in any other form. All aspects and parts of SpidexTM Database are the property of Deep Genomics and nothing in this EULA shall serve to, or should be construed to transfer any ownership rights whatsoever in SpidexTM Database to you.
3. DATABASE UPGRADES
Deep Genomics, at its discretion, may make available future upgrades to the ANNOVAR SpidexTM Database. The terms of this EULA will govern any future upgrades or updates provided by Deep Genomics in relation to the ANNOVAR SpidexTM Database unless such updates or upgrades are accompanied by separate license.
4. PUBLICATIONS
You have the right to publish experimental data or results generated through your use of the ANNOVAR SpidexTM Database in scientific manuscripts and conference abstracts, posters, or presentations (“Publication Events”). You shall acknowledge your use of the SpidexTM Database as the source of such data or results in all Publication Events by citing the following publication:
H.Y.Xiong,B.Alipanahi,L.J.Lee,H.Bretschneider,D.Merico,R.K.C.Yuen,Y.Hua,S.Gueroussov, H. S. Najafabadi, T. R. Hughes, Q. D. Morris, Y. Barash, A. R. Krainer, N. Jojic, S. W. Scherer, B. J. Blencowe and B. J. Frey. The human splicing code reveals new insights into the genetic determinants of disease. Science Express DOI: 10.1126/science.1254806, December 2014, Science 347:6218, January 2015. (Deep Genomics is the exclusive licensee of the intellectual property contained therein and associated therewith).
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6. DISCLAIMER
DEEP GENOMICS LICENSES, AND YOU ACCEPT THE ANNOVAR SPIDEXTM DATABASE UNDER THE TERMS OF THIS EULA "AS IS." DEEP GENOMICS PROVIDES NO WARRANTIES AS TO THE FUNCTION OR USE OF THE ANNOVAR SPIDEXTM DATABASE, WHETHER EXPRESS, IMPLIED, OR STATUTORY, INCLUDING, WITHOUT LIMITATION, ANY IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR PARTICULAR PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF ANNOVAR SPIDEXTM DATABASE RESTS WITH YOU. DEEP GENOMICS DOES NOT WARRANT THAT THE FUNCTIONS CONTAINED IN OR PERFORMED BY THE ANNOVAR SPIDEXTM DATABASE WILL MEET YOUR REQUIREMENTS OR THAT THE ANNOVAR SPIDEXTM DATABASE WILL FUNCTION ERROR FREE.
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9. ACCESS, TERM, AND TERMINATION
9.1. Access. You shall receive access to the ANNOVAR SpidexTM Database on the ANNOVAR servers after completing your profile. The profile submission requires your Institution name, complete mailing address, the internet protocol (IP) address of your Institution (for the purposes of secure authentication as an ANPEU), your name, your Institution email address and your phone number.
9.2. Term and Termination. This EULA is effective as of the activation date of your profile on ANNOVAR, as described in Section 9.1 above, until terminated. Deep Genomics may terminate this EULA with or without cause and without notice. Upon termination of this EULA your access to the ANNOVAR SpidexTM Database will cease immediately. Sections 1.2, 2, 5, 7.1, 8, 9.2 and 10 shall survive termination of this EULA.
10. GENERAL PROVISIONS
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