changeset 2:99517734aa65 draft default tip

Uploaded

--- a/interproscan.xml	Sun Jun 23 07:38:53 2013 -0400
+++ b/interproscan.xml	Sun Jun 23 07:41:05 2013 -0400
@@ -112,14 +112,12 @@
 Tools
 -----
 
-**PROSITE patterns**::
-
+**PROSITE patterns**
  Some biologically significant amino acid patterns can be summarised in
  the form of regular expressions.
  ScanRegExp (by [e-mail]).
 
-**PROSITE profiles**::
-
+**PROSITE profiles**
  There are a number of protein families as well as functional or
  structural domains that cannot be detected using patterns due to their extreme
  sequence divergence, so the use of techniques based on weight matrices
@@ -130,8 +128,7 @@
  co-workers.
  pfscan from the Pftools package (by [e-mail]).
 
-**PRINTS**::
-
+**PRINTS**
  The PRINTS database houses a collection of protein family fingerprints.
  These are groups of motifs that together are diagnostically more
  powerful than single motifs by making use of the biological context inherent in a
@@ -140,8 +137,7 @@
  protein super-families.
  FingerPRINTScan (Scordis P. et al., 1999).
 
-**PFAM**::
-
+**PFAM**
  Pfam is a database of protein domain families. Pfam contains curated
  multiple sequence alignments for each family and corresponding hidden
  Markov models (HMMs) (Eddy S.R., 1998). 
@@ -151,8 +147,7 @@
  hmmpfam from the HMMER2.3.2 package (by Sean Eddy,
  [e-mail], http://hmmer.wustl.edu).
 
-**PRODOM**::
-
+**PRODOM**
  ProDom is a database of protein domain families obtained by automated
  analysis of the SWISS-PROT and TrEMBL protein sequences. It is useful
  for analysing the domain arrangements of complex protein families and the
@@ -163,8 +158,7 @@
  and Yoann Beausse [e-mail])
  a wrapper on top of the Blast package (Altschul S.F. et al., 1997).
 
-**SMART**::
-
+**SMART**
  SMART (a Simple Modular Architecture Research Tool) allows the
  identification and annotation of genetically mobile domains and the
  analysis of domain architectures. These domains are extensively
@@ -174,8 +168,7 @@
  hmmpfam from the HMMER2.3.2 package (by Sean Eddy,
  [e-mail], http://hmmer.wustl.edu).
 
-**TIGRFAMs**::
-
+**TIGRFAMs**
  TIGRFAMs are a collection of protein families featuring curated multiple
  sequence alignments, Hidden Markov Models (HMMs) and associated
  information designed to support the automated functional identification
@@ -187,40 +180,35 @@
  hmmpfam from the HMMER2.3.2 package (by Sean Eddy,
  [e-mail], http://hmmer.wustl.edu).
 
-**PIR SuperFamily**::
-
+**PIR SuperFamily**
  PIR SuperFamily (PIRSF) is a classification system based on evolutionary
  relationship of whole proteins.
  hmmpfam from the HMMER2.3.2 package (by Sean Eddy,
  [e-mail], http://hmmer.wustl.edu).
 
-**SUPERFAMILY**::
-
+**SUPERFAMILY**
  SUPERFAMILY is a library of profile hidden Markov models that represent
  all proteins of known structure, based on SCOP.
  hmmpfam/hmmsearch from the HMMER2.3.2 package (by Sean Eddy,
  [e-mail], http://hmmer.wustl.edu).
  Optionally, predictions for coiled-coil, signal peptide cleavage sites
- (SignalP v3) and TM helices (TMHMM v2) are supported (See the FAQs file
- for details).
-
-**GENE3D**::
+ (SignalP v3) and TM helices (TMHMM v2) are supported (See the FAQs file for details).
 
-  Gene3D is supplementary to the CATH database. This protein sequence database
-  contains proteins from complete genomes which have been clustered into protein
-  families and annotated with CATH domains, Pfam domains and functional
-  information from KEGG, GO, COG, Affymetrix and STRINGS.
-  hmmpfam from the HMM2.3.2 package (by Sean Eddy,
-  [e-mail], http://hmmer.wustl.edu).
+**GENE3D**
+ Gene3D is supplementary to the CATH database. This protein sequence database
+ contains proteins from complete genomes which have been clustered into protein
+ families and annotated with CATH domains, Pfam domains and functional
+ information from KEGG, GO, COG, Affymetrix and STRINGS.
+ hmmpfam from the HMM2.3.2 package (by Sean Eddy,
+ [e-mail], http://hmmer.wustl.edu).
 
-**PANTHER**::
-
-  The PANTHER (Protein ANalysis THrough Evolutionary Relationships)
-  Classification System was designed to classify proteins (and their genes)
-  in order to facilitate high-throughput analysis.
-  hmmsearch from the HMM2.3.2 package (by Sean Eddy,
-  [e-mail], http://hmmer.wustl.edu).
-  and blastall from the Blast package (Altschul S.F. et al., 1997).
+**PANTHER**
+ The PANTHER (Protein ANalysis THrough Evolutionary Relationships)
+ Classification System was designed to classify proteins (and their genes)
+ in order to facilitate high-throughput analysis.
+ hmmsearch from the HMM2.3.2 package (by Sean Eddy,
+ [e-mail], http://hmmer.wustl.edu).
+ and blastall from the Blast package (Altschul S.F. et al., 1997).
 
 ----------
 References