From 7fd5a3b7a544114fa9e867fb4088a4b0b1ee9871 Mon Sep 17 00:00:00 2001 From: jprocter Date: Fri, 26 Jan 2007 10:24:08 +0000 Subject: [PATCH] preliminary documentation for DNA->protein codon features and EMBL coding region parsing --- help/html/features/codingfeatures.html | 16 ++++++++++++++++ help/html/features/seqmappings.html | 22 ++++++++++++++++++++++ 2 files changed, 38 insertions(+) create mode 100644 help/html/features/codingfeatures.html create mode 100644 help/html/features/seqmappings.html diff --git a/help/html/features/codingfeatures.html b/help/html/features/codingfeatures.html new file mode 100644 index 0000000..a828545 --- /dev/null +++ b/help/html/features/codingfeatures.html @@ -0,0 +1,16 @@ + + +DNA Sequence Coding Region Definition + + +

DNA Sequence Coding Region Definition

+

Jalview includes the standard DNA codon translation table in +order to be able to dynamically translate cDNA to its expressed +protein sequence. DNA Sequence Coding Regions are sequence +features that can be defined on any DNA sequence in order to +mark stretches of cDNA that will be concatenated to form the +series of codons that are translated by the " +Calculate→Translate cDNA" menu function. +

+ + \ No newline at end of file diff --git a/help/html/features/seqmappings.html b/help/html/features/seqmappings.html new file mode 100644 index 0000000..46fcd59 --- /dev/null +++ b/help/html/features/seqmappings.html @@ -0,0 +1,22 @@ + + +Mapping Between Different Sequences + + +

Mapping Between Different Sequences

+

A new feature in Jalview 2.8 is the ability to map +between sequences in different domains, based on alignment, +or by the use of explicit mappings provided by databases. +

+

The most familiar mapping is the one used to identify +the coordinates corresponding to a displayed sequence when +viewing a PDB file associated with a sequence (see +"Viewing PDB Files" +for more information.

+

The newest form of mapping supported by Jalview is the +correspondence between DNA and protein sequences. This mapping +can be imported directly from EMBL and EMBLCDS database records +retrieved by the Sequence Fetcher, +or by the definition of coding regions. + + \ No newline at end of file -- 1.7.10.2