Update family building text

docs/source/building-families.rst

@@ -1,33 +1,38 @@
 Building Rfam families
 ======================
 
-Rfamseq database
+*rfamseq* database
 ----------------
 
 The underlying nucleotide sequence database from which we build our
-families (known as rfamseq) is derived from the `EMBL nucleotide database <http://www.ebi.ac.uk/embl/>`_.
-We include EMBL Standard (STD) and Whole Genome Shotgun (WGS) data
+families (known as *rfamseq*) is derived from the `European Nucleotide Archive <http://www.ebi.ac.uk/ena/>`_.
+
+We include Standard (STD) and Whole Genome Shotgun (WGS) data
 classes. This includes all the environmental sample sequences (ENV)
 but we currently exclude the patented (PAT) and synthetic (SYN)
-divisions.  You should note that rfamseq does NOT include Expressed
+divisions. You should note that *rfamseq* does NOT include Expressed
 Sequence Tag (EST) or Genome Survey Sequence (GSS) data classes.
 
-Rfamseq is usually updated with each major Rfam release, e.g., 8.0, 9.0.
-You can find out the the EMBL version currently in use in the
-release README file on our `FTP site <ftp://ftp.ebi.ac.uk/pub/databases/Rfam/CURRENT">`_.
+*rfamseq* is usually updated with each major Rfam release, e.g., 8.0, 9.0.
+You can find out the ENA release currently in use in the
+`README file <ftp://ftp.ebi.ac.uk/pub/databases/Rfam/CURRENT/README>`_ on our FTP site.
 
 Seed alignments and secondary structure annotation
 --------------------------------------------------
 
-Our seed alignments are small, curated sets of representative sequences
+Our **seed alignments** are small, curated sets of representative sequences
 for each family, as opposed to an alignment of all known members. The
-seed alignment also has as a secondary structure annotation, which
+seed alignment also has as a **secondary structure** annotation, which
 represents the conserved secondary structure for these sequences.
 
-The ideal basis for a new family is an RNA element that has some
-known functional classification, is evolutionarily conserved, and has
-evidence for a secondary structure. In order to build a new family, we
-must first obtain at least one experimentally validated example from
+The ideal basis for a new family is an RNA element that:
+
+* has some known functional classification
+* is evolutionarily conserved
+* has evidence for a secondary structure
+
+In order to build a new family, we
+must first obtain at least one **experimentally validated example** from
 the published literature. If any other homologues are identified in the
 literature, we will add these to the seed. Alternatively, if these are
 not available, we will try to identify others members either by
@@ -38,7 +43,7 @@ secondary structure annotation provided in the literature. If this is
 the case, we will cite the source of both the alignment and the
 secondary structure. You should note that the structure annotations
 obtained from the literature may be experimentally validated or they
-may be RNA folding predictions (commonly `MFOLD <http://mfold.bioinfo.rpi.edu/cgi-bin/rna-form1-2.3.cgi>`_).
+may be RNA folding predictions (commonly `Mfold <http://unafold.rna.albany.edu/?q=mfold>`_).
 Unfortunately, we do not discriminate between these two cases when we
 site the PubMed Identifier (PMID) and you will need to refer to the
 original publications to clarify.
@@ -55,7 +60,8 @@ author on the list will be the most recent editor of the secondary
 structure. You can
 find the method we have used for the seed alignment or the secondary
 structure annotation in the **SE** and **SS**
-lines of the Stockholm format or in the curation information pages.
+lines of the `Stockholm format <https://en.wikipedia.org/wiki/Stockholm_format>`_
+or in the curation information pages.
 
 Covariance Models
 -----------------
@@ -64,10 +70,10 @@ From the seed alignment, we use the `Infernal software <http://eddylab.org/infer
 probabilistic model (covariance model or CM) for this family. Useful
 references on stochastic free grammars and covariance models can be
 found in the `citing Rfam <TODO>`_
-section. This model is then used to search the rfamseq
+section. This model is then used to search the *rfamseq*
 database for other possible homologs.
 
-Searching a nucleotide database as larger as rfamseq with a covariance
+Searching a nucleotide database as larger as *rfamseq* with a covariance
 model is hugely computationally expensive. In order to do this in
 reasonable time, we use sequence based filters to prune the search
 space prior to applying the CMs. Please refer to the recent Rfam
@@ -76,10 +82,10 @@ publication for more details on how we implement this.
 Expanding the seed (iteration)
 ------------------------------
 
-If the CM search of rfamseq identifies any homologs that we believe
+If the CM search of *rfamseq* identifies any homologs that we believe
 would improve the seed, we use the Infernal software (cmalign) to
 add these sequences to the seed alignment. From the new seed, the CM
-is re-built and re-searched against rfamseq. We refer to this process
+is re-built and re-searched against *rfamseq*. We refer to this process
 of expanding the seed using Infernal searching as "iteration". We
 continue to iterate the seed until we have good resolution
 between real and false hits and cannot improve the seed membership
@@ -88,9 +94,9 @@ further.
 Important points to remember about our seed alignments
 ------------------------------------------------------
 
-* We can only build families using the sequences in rfamseq
+* We can only build families using the sequences in *rfamseq*
 * We can only build a family where we can identify more than one
-  sequence in rfamseq
+  sequence in *rfamseq*
 * Sequences in the seed cannot be manually altered in any way,
   e.g. no manual excision of introns, no editing of sequencing errors,
   no marking up modified nucleotides etc
@@ -108,20 +114,17 @@ Important points to remember about our seed alignments
 Rfam full alignments
 --------------------
 
-The Rfam full alignments contain all of the sequences in rfamseq that
+The Rfam full alignments contain all of the sequences in *rfamseq* that
 we can identify as members of the family. The alignment is generated by
-searching the covariance model for the family against the rfamseq
+searching the covariance model for the family against the *rfamseq*
 database. Matches that score above a curated threshold are aligned to
 the CM to produce the full alignment. All sequences in the seed will
 also be present in the full  alignment. You should read the
 `curation information <TODO>`_ pages for details of bit scores and gathering
 thresholds.
 
 As of Rfam 12.0, we no longer automatically generate full alignments for
-each Rfam family. You can use our Sunbursts (under the Species tab) to
-generate alignments for the sequences of your choice for families with full
-alignments of less than 1000 sequences, or you may download the Rfam CM and
-generate your own alignments.
+each Rfam family. You may download the Rfam CM and generate your own alignments.
 
 Family annotation
 -----------------