Recent changes to describing_TE_sequences

describing_TE_sequences modified by Robert Kofler

Robert Kofler — Thu, 18 Oct 2018 11:59:13 -0000

--- v41
+++ v42
@@ -139,7 +139,7 @@
 **Note** Overlapping deletions (e.g. *\[4..6,4..12\]*) are not causing an error. Every base will only be deleted once.

 ### deletions and strand information
-Deletions are introduced before reverse complimenting the TE. The rationale is that many TE have distinct truncations that always occur at the same position. For example, an important variant has been described for the P-element (2907bp length): the KP-element where the bases 808-2560 of the P-element are deleted. The KP can be generated with the syntax *kp=pelement\[808-2560\]+* or the reverse complement with *kp=pelement\[808-2560\]-*
+Deletions are introduced before reverse complimenting the TE. The rationale is that many TE have distinct truncations that always occur at the same position. For example, an important variant has been described for the P-element (2907bp length): the KP-element where the bases 808-2560 of the P-element are deleted. The KP can be generated with the syntax *kp=pelement\[808..2560\]+* or the reverse complement with *kp=pelement\[808..2560\]-*

 As another example, given:

describing_TE_sequences modified by Robert Kofler

Robert Kofler — Tue, 25 Jul 2017 10:15:13 -0000

--- v40
+++ v41
@@ -139,9 +139,9 @@
 **Note** Overlapping deletions (e.g. *\[4..6,4..12\]*) are not causing an error. Every base will only be deleted once.

 ### deletions and strand information
-Deletions are introduced before reverse complimenting the TE. The rationale is that many TE have distinct truncations that always occur at the same position, and only a single syntax should be used to generate these truncated copies; For example, an important variant has been described for the P-element (2907bp length): the KP-element where the bases 808-2560 are deleted. The KP can be generated with the syntax *kp=pelement\[808-2560\]*
-
-for example given:
+Deletions are introduced before reverse complimenting the TE. The rationale is that many TE have distinct truncations that always occur at the same position. For example, an important variant has been described for the P-element (2907bp length): the KP-element where the bases 808-2560 of the P-element are deleted. The KP can be generated with the syntax *kp=pelement\[808-2560\]+* or the reverse complement with *kp=pelement\[808-2560\]-*
+
+As another example, given:

 ~~~~~~
 chasis="123456789"
@@ -184,7 +184,7 @@
 ## diverged insertions 

 ###basics
-It is possible to introduced random mutations into a sequence by simply providing the percentage of the divergence after the strand:
+It is possible to introduced random mutations (base substitutions) into a sequence by simply providing the percentage of the divergence after the strand:

 For example given a pgd-file:

@@ -225,7 +225,7 @@

 ### basics

-Nested insertions must be provided in curly brackets after the strand (*+* or *-*) of the TE insertion.
+Nested insertions must be provided in curly brackets after the strand (*+* or *-*).

 given the pgd-file

@@ -318,7 +318,7 @@

 ### nested insetions and TSDs

-A TSD of a nested insertion may be simply provided by adding say 3bp after declaration of the nested insertion.
+A TSD of a nested insertion may be  provided by adding say 3bp after declaration of the nested insertion.

 Given a pgd-file:

@@ -338,7 +338,7 @@

 ### nested insertions and sequence divergence

-Nested insertions and sequence divergence may be combined. Note that random mutations will only be introduced into the parent sequence not into the nested child insertions. This allows a more fine graind control and avoids multiple mutations of nested sequences.
+Nested insertions and sequence divergence may be combined. Note that random mutations will only be introduced into the parent sequence not into the nested child insertions. This allows a more fine graind control and avoids multiple rounds of mutations for nested sequences.

 Given the pgd-file:

@@ -377,11 +377,11 @@
 12345TTACCCCA6789
 ~~~~~

-**Note** : firstly the truncated sequence is generated (*TTtttAA*  -> *TTAA*) and secondly the child-TE is inserted into the parent sequence.  Thus when computing the insertion position of the child-TE (pelement at position 3 of hobo) the truncated regions are ignored.  
+**Note** : first the truncated sequence is generated (*TTtttAA*  -> *TTAA*) and second the child-TE is inserted into the parent sequence.  Thus when computing the insertion position of the child-TE (position 3 of hobo) the truncated regions are ignored.  

 ### multiple nested insertions

-Several child insertions nested into a parent may be specified and must be separated by a coma (*,*).
+Several nested insertions may be specified; They must be separated by a coma (*,*).

 Given the pgd-file:

@@ -402,7 +402,7 @@

 ### deeply nested insertions
-Our domain specific language also allows to provide nested insertions within nested insertions (up to an arbitrary depth).
+Our domain specific language also allows to specify recursively nested insertions (up to an arbitrary depth).

 For example given the TSD file

@@ -448,14 +448,14 @@
 ~~~~~~

-**Note** the characters 0123456789 and atcg (instead of uppercase ATCG) have only be used for illustrative purposes. Solely the characters ATCG are allowed for real data, as the reverse complement and mutations require ATCG.
-
-
-
-
-
-
-
-
-
-
+**Note** the characters 0123456789 and atcg (instead of uppercase ATCG) have only be used for illustrative purposes. Solely the characters ATCG are allowed for real data.
+
+
+
+
+
+
+
+
+
+

describing_TE_sequences modified by Robert Kofler

Robert Kofler — Tue, 25 Jul 2017 10:01:11 -0000

--- v39
+++ v40
@@ -114,7 +114,7 @@
 12345AAGG6789
 ~~~~~

-The syntax *\[3..6\]* specifies that the bases 3 to 6 should be removed from *hobo*.
+The syntax *hobo\[3..6\]* specifies that the bases 3 to 6 should be removed from *hobo*.

 ### multiple deletions
@@ -139,7 +139,7 @@
 **Note** Overlapping deletions (e.g. *\[4..6,4..12\]*) are not causing an error. Every base will only be deleted once.

 ### deletions and strand information
-Deletions are introduced before reverse complimenting the  a TE. The rationale is that many TE have distinct truncations that always occur at the same positin within the TE, for example the P-element (2907bp length) the KP-element has been described with the bases 808-2560 being removed.
+Deletions are introduced before reverse complimenting the TE. The rationale is that many TE have distinct truncations that always occur at the same position, and only a single syntax should be used to generate these truncated copies; For example, an important variant has been described for the P-element (2907bp length): the KP-element where the bases 808-2560 are deleted. The KP can be generated with the syntax *kp=pelement\[808-2560\]*

 for example given:

describing_TE_sequences modified by Robert Kofler

Robert Kofler — Tue, 25 Jul 2017 09:52:12 -0000

--- v38
+++ v39
@@ -4,7 +4,7 @@
 However, based on this set of initial TE sequences (e.g the consensus sequences of TE families), our domain specific language allows to define **arbitrary complex derived sequences**  having, for example, large deletions (e.g. the KP element is a truncated P-element),  complex **nested insertions**,   and sequence divergence.

-Within the pgd-file, derivate sequences may either be defined in the header as in the following example:
+Based on the pgd-file, derivate sequences may either be defined in the header as in the following example:

 ~~~~~
 hobo="TTT"
@@ -14,7 +14,7 @@

 where we define the sequence *nesthobo* as a *hobo* insertion having a nested *roo* insertion at the second position.

-Alternatively derivate sequences may be directly defined at the insertion site as in the following example pgd-file
+Alternatively derivate sequences may be directly defined at the insertion site as in the following example of a pgd-file

 ~~~~~
 hobo="TTT"
@@ -22,11 +22,11 @@
 9 * * * * * hobo+{2:roo}
 ~~~~~

-Mostly it will not make a difference which of these two strategies is used. It will however make a difference when a sequence divergence is provided. A  TE defined in the header will only be mutated once, whereas each TE defined at the insertion site will be mutated separately. For more details on defining the sequences see [describing_TE_landscapes]
+Mostly it will not make a difference which of these two strategies is used. It will however only make a difference when a sequence divergence is provided. A diverged TE sequence that is defined in the header will only be mutated once, whereas each TE defined at the insertion site will be mutated separately.  For more details on defining the sequences see [describing_TE_landscapes]

 # A domain specific language for defining insertion sequences

-In the following examples we use a chasis consisting of the sequence **"123456789"**. Of  course, usually a **DNA** sequence has to be provided but this numerical sequence tremendously helps to explain the domain specific language. All examples here have been tested and most are also implemented as unit-tests, so their proper execution is guaranteed.
+In the following examples we use a chasis consisting of the sequence **"123456789"**.  Of course, usually a **DNA** sequence has to be provided but this numerical sequence tremendously helps to explain our domain specific language. All shown examples  have been tested and most are also implemented as unit-tests, so their proper execution is ensured.

 ## Strand

@@ -71,8 +71,9 @@
 12TTT234567AAA6789
 ~~~~~

-Per default the TSD of the parent TE is used. If a TE has no parent zero is used.
-**Note** that the bases left to the insertion site are used for the TSD. In other words when choosing the insertion site, pick the site at the rightmost end of the TSD.
+Per default the TSD of the parent TE is used. If a TE has no parent a TSD of zero is used.
+
+**Note**  the bases left to the insertion site are used for the TSD. In other words when choosing the insertion site, pick the site at the rightmost end of the TSD.

 ### per default the TSD of the parent is used

@@ -92,12 +93,12 @@
 12TTT1234567AAA6789
 ~~~~~~

-The parent is *h* with a TSD=2; The two kids *h_plus* and *h_minus* inherit the TSD of 2bp. If the child should have another TSD, just redefine it (e.g. specify *h_plus=h+3bp*)
+The parent is *h* with a TSD=2; The two kids *h_plus* and *h_minus* inherit the TSD of 2bp. If another TSD should be used for the child, just provide a new TSD (e.g. specify *h_plus=h+3bp*)

 ## deletions/truncations
 ### basics

-Deletions or truncations within TEs may be specified witht the square brackets. Specifiy the regions that will be deleted. Multiple regions may be specified.
+Deletions or truncations within TEs may be specified using square brackets. Specify the regions that will be deleted. Multiple regions may be specified.

 For examle, given the pgd-file:

@@ -113,7 +114,7 @@
 12345AAGG6789
 ~~~~~

-This deletion of hobo specifies that the base 3 to 6 should be removed.
+The syntax *\[3..6\]* specifies that the bases 3 to 6 should be removed from *hobo*.

 ### multiple deletions

describing_TE_sequences modified by Robert Kofler

Robert Kofler — Sun, 23 Jul 2017 19:54:44 -0000

--- v37
+++ v38
@@ -138,7 +138,7 @@
 **Note** Overlapping deletions (e.g. *\[4..6,4..12\]*) are not causing an error. Every base will only be deleted once.

 ### deletions and strand information
-Deletions are introduced before changing the strand of a TE. The rationale is that for example the distinct truncation of the KP-element  always occurs at the same position within the P-element.
+Deletions are introduced before reverse complimenting the  a TE. The rationale is that many TE have distinct truncations that always occur at the same positin within the TE, for example the P-element (2907bp length) the KP-element has been described with the bases 808-2560 being removed.

 for example given:

describing_TE_sequences modified by Robert Kofler

Robert Kofler — Sun, 23 Jul 2017 19:50:38 -0000

--- v36
+++ v37
@@ -26,7 +26,7 @@

 # A domain specific language for defining insertion sequences

-In the following demonstrations we use a chasis consisting of the sequence **"123456789"**. Of  course, usually a **DNA** sequence has to be provided but this numerical sequence tremendously helps to explain the domain specific language. All examples here have been tested and most are also implemented as unit-tests, so their proper execution is guaranteed.
+In the following examples we use a chasis consisting of the sequence **"123456789"**. Of  course, usually a **DNA** sequence has to be provided but this numerical sequence tremendously helps to explain the domain specific language. All examples here have been tested and most are also implemented as unit-tests, so their proper execution is guaranteed.

 ## Strand

describing_TE_sequences modified by Robert Kofler

Robert Kofler — Sun, 23 Jul 2017 19:50:11 -0000

--- v35
+++ v36
@@ -71,7 +71,7 @@
 12TTT234567AAA6789
 ~~~~~

-Per default the TSD of the parent is used. If a TE has no parent zero is used.
+Per default the TSD of the parent TE is used. If a TE has no parent zero is used.
 **Note** that the bases left to the insertion site are used for the TSD. In other words when choosing the insertion site, pick the site at the rightmost end of the TSD.

 ### per default the TSD of the parent is used

describing_TE_sequences modified by Robert Kofler

Robert Kofler — Sun, 23 Jul 2017 19:48:29 -0000

--- v34
+++ v35
@@ -22,7 +22,7 @@
 9 * * * * * hobo+{2:roo}
 ~~~~~

-Mostly it will not make a difference which of these two strategies is used. It will however make a difference when a sequence divergence is provided. A  TE defined in the header will only be mutated once, whereas each TE defined at the insertion site will be mutated separately. For more details on defining the sequences
+Mostly it will not make a difference which of these two strategies is used. It will however make a difference when a sequence divergence is provided. A  TE defined in the header will only be mutated once, whereas each TE defined at the insertion site will be mutated separately. For more details on defining the sequences see [describing_TE_landscapes]

 # A domain specific language for defining insertion sequences

describing_TE_sequences modified by Robert Kofler

Robert Kofler — Thu, 08 Jun 2017 15:39:27 -0000

--- v33
+++ v34
@@ -425,7 +425,7 @@

 ## Arbitrary complex scenarios

-It is possible to combine deletions, nested insertions, sequence divergence and deeply nested insertions in any arbitrary way.
+In the final example we demonstrate that it is possible to combine deletions, nested insertions, sequence divergence and deeply nested insertions in any arbitrary way.

 For example given the pgd-file:

describing_TE_sequences modified by Robert Kofler

Robert Kofler — Thu, 08 Jun 2017 15:38:49 -0000

--- v32
+++ v33
@@ -447,14 +447,14 @@
 ~~~~~~

-**Note** the characters 0123456789 and atcg (instead of uppercase ATCG) have only used for demonstration purposes. Only the characters ATCG are allowed for real data, as the reverse complement and mutations are only supported for ATCG.
-
-
-
-
-
-
-
-
-
-
+**Note** the characters 0123456789 and atcg (instead of uppercase ATCG) have only be used for illustrative purposes. Solely the characters ATCG are allowed for real data, as the reverse complement and mutations require ATCG.
+
+
+
+
+
+
+
+
+
+