diff --git a/.DS_Store b/.DS_Store deleted file mode 100644 index 6d00682..0000000 Binary files a/.DS_Store and /dev/null differ diff --git a/.gitignore b/.gitignore index 6dd84af..c6508e5 100644 --- a/.gitignore +++ b/.gitignore @@ -1,2 +1,3 @@ env *idea +.DS_Store diff --git a/docs/source/citing-rfam.rst b/docs/source/citing-rfam.rst index 7f5596d..6c0eaf3 100644 --- a/docs/source/citing-rfam.rst +++ b/docs/source/citing-rfam.rst @@ -1,7 +1,7 @@ Citing Rfam =========== -Rfam makes use of a large amount of publicly available data, especially published multiple sequence alignments and secondary structures, and repackages these data in a single searchable and sustainable resource. We have made every effort to credit individual sources on family pages. If you find any of the data presented here useful, please also be sure to credit the primary source also. +Rfam makes use of a large amount of publicly available data, especially published multiple sequence alignments and secondary structures, and repackages these data in a single searchable and sustainable resource. We have made every effort to credit individual sources on family pages. If you find any of the data presented here useful, please be sure to credit the primary source as well. Rfam references --------------- @@ -14,13 +14,9 @@ Rfam references | **Nucleic Acids Research** (2020) doi: 10.1093/nar/gkaa1047 `Non‐coding RNA analysis using the Rfam database `_ - | I. Kalvari, E.P. Nawrocki, J. Argasinska, N. Quinones‐Olvera, R.D. Finn, A. Bateman and A.I. Petrov + | I. Kalvari, E.P. Nawrocki, J. Argasinska, N. Quinones‐Olvera, R.D. Finn, A. Bateman, and A.I. Petrov | **Current Protocols in Bioinformatics** (2018) e51. doi: 10.1002/cpbi.51 -`Computational strategies to combat COVID-19: useful tools to accelerate SARS-CoV-2 and coronavirus research `_ - | Hufsky et al. - | **Briefings in Bioinformatics** (2020). doi: 10.1093/bib/bbaa232 - `Rfam 13.0: shifting to a genome-centric resource for non-coding RNA families `_ | I. Kalvari, J. Argasinska, N. Quinones-Olvera, E.P. Nawrocki, E. Rivas, S.R. Eddy, A. Bateman, R.D. Finn, and A.I. Petrov | **Nucleic Acids Research** (2017) doi: 10.1093/nar/gkx1038 @@ -30,29 +26,34 @@ Rfam references | **Nucleic Acids Research** (2014) doi: 10.1093/nar/gku1063 `Rfam 11.0: 10 years of RNA families `_ - | S.W. Burge, J. Daub, R. Eberhardt, J. Tate, L. Barquist, E.P. Nawrocki, S.R. Eddy, P.P. Gardner and A. Bateman. + | S.W. Burge, J. Daub, R. Eberhardt, J. Tate, L. Barquist, E.P. Nawrocki, S.R. Eddy, P.P. Gardner, and A. Bateman. | **Nucleic Acids Research** (2012) doi: 10.1093/nar/gks1005 `Rfam: Wikipedia, clans and the “decimal” release `_ - | P.P. Gardner, J. Daub, J. Tate, B.L. Moore, I.H. Osuch, S. Griffiths-Jones, R.D. Finn, E.P. Nawrocki, D.L. Kolbe, S.R. Eddy and A. Bateman. - | **Nucleic Acids Research** (2011) doi: 10.1093/nar/gkq1129 + | P.P. Gardner, J. Daub, J. Tate, B.L. Moore, I.H. Osuch, S. Griffiths-Jones, R.D. Finn, E.P. Nawrocki, D.L. Kolbe, S.R. Eddy, and A. Bateman. + | **Nucleic Acids Research** (2011) doi: 10.1093/nar/gkq1129 -`Rfam: updates to the RNA families database `_ - | P.P. Gardner, J. Daub, J.G. Tate, E.P. Nawrocki, D.L. Kolbe, S. Lindgreen, A.C. Wilkinson, R.D. Finn, S. Griffiths-Jones, S.R. Eddy and A. Bateman - | **Nucleic Acids Research** (2009) Database Issue 37:D136-D140 +`Rfam: updates to the RNA families database `_ + | P.P. Gardner, J. Daub, J.G. Tate, E.P. Nawrocki, D.L. Kolbe, S. Lindgreen, A.C. Wilkinson, R.D. Finn, S. Griffiths-Jones, S.R. Eddy, and A. Bateman + | **Nucleic Acids Research** (2009) Database Issue 37:D136-D140 `The RNA WikiProject: community annotation of RNA families `_ - | J. Daub, P.P. Gardner, J. Tate, D. Ramsköld, M. Manske, W.G. Scott, Z. Weinberg, S. Griffiths-Jones and A. Bateman + | J. Daub, P.P. Gardner, J. Tate, D. Ramsköld, M. Manske, W.G. Scott, Z. Weinberg, S. Griffiths-Jones, and A. Bateman | **RNA** (2008) 12:2462-2464 -`Rfam: annotating non-coding RNAs in complete genomes `_ +`Rfam: annotating non-coding RNAs in complete genomes `_ | S. Griffiths-Jones, S. Moxon, M. Marshall, A. Khanna, S.R. Eddy, A. Bateman | **Nucleic Acids Research** (2005) Database Issue 33:D121-D124 -`Rfam: an RNA family database `_ - | S. Griffiths-Jones, A. Bateman, M. Marshall, A. Khanna and S.R. Eddy +`Rfam: an RNA family database `_ + | S. Griffiths-Jones, A. Bateman, M. Marshall, A. Khanna, and S.R. Eddy | **Nucleic Acids Research** (2003) 31(1):p439-441 +Other contributions +------------------- +`Computational strategies to combat COVID-19: useful tools to accelerate SARS-CoV-2 and coronavirus research `_ + | Hufsky et al. + | **Briefings in Bioinformatics** (2020) doi: 10.1093/bib/bbaa232 Covariance models and stochastic context-free grammars ------------------------------------------------------- @@ -66,7 +67,7 @@ Covariance models and stochastic context-free grammars `Computational Identification of Functional RNA Homologs in Metagenomic Data `_ | E. P. Nawrocki, S. R. Eddy - | **RNA Biology** (2013) 10:1170-1179, 2013 + | **RNA Biology** (2013) 10:1170-1179 `Infernal 1.0: Inference of RNA Alignments `_ | E.P. Nawrocki, D.L. Kolbe, S.R. Eddy @@ -78,20 +79,20 @@ Covariance models and stochastic context-free grammars `Query-dependent banding (QDB) for faster RNA similarity searches `_ | E.P. Nawrocki, S.R. Eddy - | **PLoS Computational Biology** (2007) 3(3):e56 + | **PLoS Computational Biology** (2007) 3(3):e56 `A memory-efficient dynamic programming algorithm for optimal alignment of a sequence to an RNA secondary structure `_ | S.R. Eddy - | **BMC Bioinformatics** (2002) 2(3):18 + | **BMC Bioinformatics** (2002) 2(3):18 `Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids `_ | R. Durbin, S.R. Eddy, A. Krogh, G. Mitchison | **Cambridge University Press** (1999) ISBN 0-5216-2971-3 -`tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence `_ +`tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence `_ | T.M. Lowe, S.R. Eddy | **Nucleic Acids Research** (1997) 25(5):955-964 -`RNA sequence analysis using covariance models `_ +`RNA sequence analysis using covariance models `_ | S.R. Eddy, R. Durbin | **Nucleic Acids Research** (1994) 22(11):2079-88 diff --git a/docs/source/conf.py b/docs/source/conf.py index fb14f23..a0348c1 100644 --- a/docs/source/conf.py +++ b/docs/source/conf.py @@ -70,7 +70,7 @@ # # This is also used if you do content translation via gettext catalogs. # Usually you set "language" from the command line for these cases. -language = None +language = 'en' # There are two options for replacing |today|: either, you set today to some # non-false value, then it is used: diff --git a/docs/source/contact-us.rst b/docs/source/contact-us.rst index 171319a..b160403 100644 --- a/docs/source/contact-us.rst +++ b/docs/source/contact-us.rst @@ -16,12 +16,16 @@ You can see blog posts that are specific to Rfam `here `_ feed from the Xfam blog. -Twitter -------- -You can `follow `_ the RfamDB team at EMBL-EBI. +LinkedIn +-------- +You can `follow `_ the EMBL-EBI RNA Resources team on LinkedIn. + +X +- +You can `follow `_ the RfamDB team at EMBL-EBI. Submit an alignment ------------------- diff --git a/docs/source/ftp-help.rst b/docs/source/ftp-help.rst index aab61e5..485237c 100644 --- a/docs/source/ftp-help.rst +++ b/docs/source/ftp-help.rst @@ -1,7 +1,7 @@ Rfam FTP Site ============= -The following list describes a few of the important files in the +The following list describes a few of the important files on the Rfam `FTP site `_. Some of these files may be very large (of the order of several hundred megabytes). Please check the sizes before trying to download them over a slow connection. @@ -10,30 +10,30 @@ Documentation ------------- `README `_ - Release Notes + Release Notes. `COPYING `_ - Public Domain Information for Rfam + Public Domain Information for Rfam. `USERMAN `_ - A description of the Rfam flatfile formats + A description of the Rfam flatfile formats. Sequences, Alignments, Models and Trees --------------------------------------- `Rfam.tar.gz `_ - Rfam covariance models in ascii INFERNAL format + Rfam covariance models in ASCII INFERNAL format `Rfam.seed.gz `_ Annotated seed alignments in STOCKHOLM format `Rfam.seed_tree.tar.gz `_ Annotated tree files for each seed alignment `Rfam.full_region.gz `_ List of sequence regions making up the full family membership for each family -`fasta_files `_ +`fasta_files `_ Directory containing the sequences for all significant hits per family Rfam database dumps ------------------- `database_files `_ - Directory containing MYSQL dump of the the Rfam database data, tables and mysql database schema + Directory containing a MySQL dump of the Rfam database data, tables, and schema -.. hint:: For direct access to the database please visit :ref:`database:Public MySQL Database` +.. hint:: For direct access to the database, please visit :ref:`database:Public MySQL Database` diff --git a/docs/source/index.rst b/docs/source/index.rst index 7f8c152..08bf0bb 100644 --- a/docs/source/index.rst +++ b/docs/source/index.rst @@ -58,7 +58,7 @@ We choose CC0 because: * It is most in line with the spirit of EMBL-EBI’s Terms of use and places data in the public domain without constraints. We believe that this approach to research data sharing strengthens open science and scientific progress. -* It is the best way to encourage remixing and reuse as it makes clear to any user – academic, commercial or otherwise – that the data are not owned by anyone and therefore can be used freely. +* It is the best way to encourage remixing and reuse as it makes clear to any user – academic, commercial, or otherwise – that the data are not owned by anyone and therefore can be used freely. * It saves researchers time when reusing the data, which speeds up the process of science. @@ -67,7 +67,7 @@ Rfam conforms to the EBI long-term data preservation `policy `_ and `Wellcome `_ and is developed at the `EMBL-EBI `_. +Rfam is supported by the `BBSRC `_ and `Wellcome `_, and is developed at the `EMBL-EBI `_. .. image:: images/ukri-bbsrc.png :alt: BBSRC logo diff --git a/docs/source/rfam-team.rst b/docs/source/rfam-team.rst index 2af722a..b3ef365 100644 --- a/docs/source/rfam-team.rst +++ b/docs/source/rfam-team.rst @@ -22,10 +22,11 @@ Collaborators * :raw-html:`Sean Eddy` (Harvard University) - founding developer and author of Infernal software * :raw-html:`Eric Nawrocki` (NCBI) - developer of the Infernal software * :raw-html:`Elena Rivas` (Harvard University) - developer of the R-scape software -* :raw-html:`Manja Marz` and :raw-html:`Kevin Lamkiewicz` (Friedrich Schiller University Jena) - collaborators on the :raw-html:`Rfam Viruses project` +* :raw-html:`Manja Marz`, :raw-html:`Sandra Triebel`, and :raw-html:`Kevin Lamkiewicz` (Friedrich Schiller University Jena) - collaborators on the :raw-html:`Rfam Viruses project` * :raw-html:`Sam Griffiths-Jones` (University of Manchester) - *founding Rfam project leader* and a collaborator on the :raw-html:`microRNA project` -* :raw-html:`Daniel Gautheret` and :raw-html:`Claire Toffano-Nioche` (University of Paris-Saclay) - collaborators on the :raw-html:`Rfam Cloud project` +* :raw-html:`Daniel Gautheret` and :raw-html:`Claire Toffano-Nioche` (University of Paris-Saclay) * :raw-html:`Zasha Weinberg` (University of Leipzig) - developer of the ZWD database +* :raw-html:`Michelle Scott` and Kristina Song (Université de Sherbrooke) Previous contributors --------------------- @@ -35,9 +36,9 @@ Previous contributors * :raw-html:`Rob Finn` - *Group Team Leader* * :raw-html:`Anton I. Petrov` - *former Rfam project leader* * :raw-html:`Blake A. Sweeney` - *former Rfam project leader* -* :raw-html:`Ioanna Kalvari` - *Software developer* +* :raw-html:`Ioanna Kalvari` - *former Software developer* * :raw-html:`Emma Cooke` - *former Rfam Software Developer* -* :raw-html:`Joanna Argasinska` - *Biocurator* +* :raw-html:`Joanna Argasinska` - *former Biocurator* * :raw-html:`Ruth Eberhardt` * :raw-html:`Evan Floden` * John Tate @@ -50,6 +51,6 @@ Previous contributors * Enrico Marantidis * Diana Kolbe -Rfam is a collaborative venture and we hope to be able to interact +Rfam is a collaborative venture and we hope to interact with as many people as possible to provide a quality database. Please :ref:`contact-us:Contact us` for information.