diff --git a/docs/index.rst b/docs/index.rst index 84f87bf..d7c1e3a 100755 --- a/docs/index.rst +++ b/docs/index.rst @@ -83,7 +83,7 @@ attempt to find larger sets: Finding a sequence decomposition -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In this example, we find where to cut a 50-kilobasepair sequence to create @@ -91,8 +91,8 @@ assemblable fragments with 4-basepair overhangs. We indicate that: - There should be 50 fragments, with a minimum of variance in their sizes. - The fragments overhangs should have 25-75 GC% with a 1-basepair difference - between any two overhangs (and their reverse-complement). They should also be - compatible with the 4-basepair extremities of the sequence. + between any two overhangs (and their reverse-complement). They should also be + compatible with the 4-basepair extremities of the sequence. .. code:: python @@ -104,7 +104,7 @@ assemblable fragments with 4-basepair overhangs. We indicate that: solution = selector.cut_sequence(sequence, equal_segments=50, max_radius=20, include_extremities=True) -This returns a list of dictionnaries, each representing one overhang with +This returns a list of dictionaries, each representing one overhang with properties ``o['location']`` (coordinate of the overhang in the sequence) and ``o['sequence']`` (sequence of the overhang). @@ -123,7 +123,7 @@ the overhang's positions, using the following function: display_positions=False) Sequence mutation and decomposition from a Genbank file -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ If the input sequence is a Genbank record (or a Biopython record) has locations annotated vy features feature labeled ``!cut``, GoldenHinges will attempt to @@ -135,7 +135,7 @@ Note that solutions involving base changes are penalized and solutions involving the original solution will always be prefered, so no base change will be suggested unless strictly necessary. -If the input record has `DnaChisel `_ +If the input record has `DNA Chisel `_ annotations such as ``@AvoidChanges`` or ``@EnforceTranslation``, these will be enforced to forbid some mutations. @@ -180,13 +180,13 @@ using this command: Contribute ! --------------- +------------ Golden Hinges is an open-source software originally written at the `Edinburgh Genome Foundry `_ by `Zulko `_ and `released on Github `_ -under the MIT licence. Everyone is welcome to contribute ! +under the MIT licence. Everyone is welcome to contribute! .. raw:: html