Recent changes to Toy examples

Toy examples modified by Filip Wierzbicki

Filip Wierzbicki — Tue, 29 Dec 2020 10:21:07 -0000

--- v8
+++ v9
@@ -5,6 +5,7 @@

 #Match
 Alignment between two identical sequences of transposable element annotations.
+
 **Input 1**
 ~~~
 hobo
@@ -84,6 +85,7 @@

 #Multiple shared polymorphisms
 Alignment of 5 similar sequences with a shared insertion  "x" between 2 sequences and another shared insertion "y" between 3 sequences.
+
 **Input 1**
 ~~~
 a x b c
@@ -106,7 +108,6 @@
 ~~~

 **Output**
-
 ~~~
 a - b y c
 a - b y c
@@ -115,8 +116,9 @@
 a x b - c
 ~~~

-#Segmental uplication
+#Segmental duplication
 Alignment of 2 similar sequences with a segmental duplication of "b c d" in input 1.
+
 **Input 1**
 ~~~
 a b c d b c d e 
@@ -133,9 +135,10 @@
 ~~~


-**As expected, the following scenarios could not be fully resolved: **
+#As expected, the following scenarios could not be fully resolved:
 #Inversion
 Alignment of 2 similar sequences with an inversion of "b c d" in input 1.
+
 **Input 1**
 ~~~
 a d c b e 
@@ -153,6 +156,7 @@

 #Translocation
 Alignment of 2 similar sequences with a tranlocation of "b c d" in input 1.
+
 **Input 1**
 ~~~
 a e b c d f
@@ -167,6 +171,7 @@
 a e b c d - f
 a - b c d e f
 ~~~
+
 #Nested insertion
 Alignment of 2 similar sequences with an insertion of "x" into "c" resulting in a fragmented annotation of "c" in input 1.

Toy examples modified by Filip Wierzbicki

Filip Wierzbicki — Mon, 28 Dec 2020 17:00:13 -0000

--- v7
+++ v8
@@ -29,7 +29,7 @@

 #Insertion/deletion polymorphism
-Alignment between two similar sequences of transposable element annotations with a presence/absence polymorphisms of a rooA.
+Alignment between two similar sequences of transposable element annotations with a presence/absence polymorphisms of a rooA in input 1.

 **Input 1**
 ~~~
@@ -115,9 +115,60 @@
 a x b - c
 ~~~

+#Segmental uplication
+Alignment of 2 similar sequences with a segmental duplication of "b c d" in input 1.
+**Input 1**
+~~~
+a b c d b c d e 
+~~~
+**Input 2**
+~~~
+a b c d e
+~~~

+**Output**
+~~~
+a b c d b c d e 
+a - - - b c d e
+~~~
+
+
+**As expected, the following scenarios could not be fully resolved: **
+#Inversion
+Alignment of 2 similar sequences with an inversion of "b c d" in input 1.
+**Input 1**
+~~~
+a d c b e 
+~~~
+**Input 2**
+~~~
+a b c d e
+~~~
+
+**Output**
+~~~
+a - - d c b e
+a b c d - - e
+~~~
+
+#Translocation
+Alignment of 2 similar sequences with a tranlocation of "b c d" in input 1.
+**Input 1**
+~~~
+a e b c d f
+~~~
+**Input 2**
+~~~
+a b c d e f
+~~~
+
+**Output**
+~~~
+a e b c d - f
+a - b c d e f
+~~~
 #Nested insertion
-Alignment of 2 similar sequence with an insertion of "x" into "c" resulting in a fragmented annotation of "c". 
+Alignment of 2 similar sequences with an insertion of "x" into "c" resulting in a fragmented annotation of "c" in input 1. 

 **Input 1**
 ~~~
@@ -133,4 +184,3 @@
 a b c x c d e
 a b - - c d e
 ~~~
-**As expected, this results in a false positive polymorphism of "c".**

Toy examples modified by Filip Wierzbicki

Filip Wierzbicki — Mon, 28 Dec 2020 16:27:39 -0000

--- v6
+++ v7
@@ -59,7 +59,7 @@
 **Note: For brevity of of the following examples, we replaced annotation names with single, arbitrary letters and transposed the input and output.**

-#Shared insertion
+#Shared polymorphism
 Alignment of 3 similar sequences with a shared insertion between 2 of them. The insertion is represented by a "x".

 **Input 1**
@@ -82,7 +82,7 @@
 a - b
 ~~~

-#Multiple shared insertions
+#Multiple shared polymorphisms
 Alignment of 5 similar sequences with a shared insertion  "x" between 2 sequences and another shared insertion "y" between 3 sequences.
 **Input 1**
 ~~~
@@ -116,3 +116,21 @@
 ~~~


+#Nested insertion
+Alignment of 2 similar sequence with an insertion of "x" into "c" resulting in a fragmented annotation of "c". 
+
+**Input 1**
+~~~
+a b c x c d e
+~~~
+**Input 2**
+~~~
+a b c d e
+~~~
+
+**Output**
+~~~
+a b c x c d e
+a b - - c d e
+~~~
+**As expected, this results in a false positive polymorphism of "c".**

Toy examples modified by Filip Wierzbicki

Filip Wierzbicki — Mon, 28 Dec 2020 16:00:55 -0000

--- v5
+++ v6
@@ -18,7 +18,7 @@

 **command**
 ~~~
-python /Users/filipwierzbicki/Documents/PhD_Project/Bioinformatics/manna-code/cluster-msa.py --gap 0.09 --mm 0.1 --match 0.2 --input-format toy --clusters "1,2" --sample-IDs "1,2"|grep -v '^#'|awk '{print $1,$4}'
+python manna-code/cluster-msa.py --gap 0.09 --mm 0.1 --match 0.2 --input-format toy --clusters "1,2" --sample-IDs "1,2"|grep -v '^#'|awk '{print $1,$4}'
 ~~~

 **output**
@@ -28,7 +28,7 @@
 ~~~


-#Insertion/deletion
+#Insertion/deletion polymorphism
 Alignment between two similar sequences of transposable element annotations with a presence/absence polymorphisms of a rooA.

 **Input 1**
@@ -45,7 +45,7 @@

 **command**
 ~~~
-python /Users/filipwierzbicki/Documents/PhD_Project/Bioinformatics/manna-code/cluster-msa.py --gap 0.09 --mm 0.1 --match 0.2 --input-format toy --clusters "1,2" --sample-IDs "1,2"|grep -v '^#'|awk '{print $1,$4}'
+python manna-code/cluster-msa.py --gap 0.09 --mm 0.1 --match 0.2 --input-format toy --clusters "1,2" --sample-IDs "1,2"|grep -v '^#'|awk '{print $1,$4}'
 ~~~

 **output**
@@ -56,7 +56,63 @@
 ~~~


+**Note: For brevity of of the following examples, we replaced annotation names with single, arbitrary letters and transposed the input and output.**


+#Shared insertion
+Alignment of 3 similar sequences with a shared insertion between 2 of them. The insertion is represented by a "x".
+
+**Input 1**
+~~~
+a x b
+~~~
+**Input 2**
+~~~
+a x b
+~~~
+**Input 3**
+~~~
+a b
+~~~
+
+**output**
+~~~
+a x b
+a x b
+a - b
+~~~
+
+#Multiple shared insertions
+Alignment of 5 similar sequences with a shared insertion  "x" between 2 sequences and another shared insertion "y" between 3 sequences.
+**Input 1**
+~~~
+a x b c
+~~~
+**Input 2**
+~~~
+a x b c
+~~~
+**Input 3**
+~~~
+a b y c
+~~~
+**Input 4**
+~~~
+a b y c
+~~~
+**Input 5**
+~~~
+a b y c
+~~~
+
+**Output**
+
+~~~
+a - b y c
+a - b y c
+a - b y c
+a x b - c
+a x b - c
+~~~

Toy examples modified by Filip Wierzbicki

Filip Wierzbicki — Mon, 28 Dec 2020 15:07:58 -0000

--- v4
+++ v5
@@ -8,7 +8,7 @@
 **Input 1**
 ~~~
 hobo
-P-ele
+Pele
 ~~~
 **Input 2**
 ~~~
@@ -28,7 +28,35 @@
 ~~~

+#Insertion/deletion
+Alignment between two similar sequences of transposable element annotations with a presence/absence polymorphisms of a rooA.
+
+**Input 1**
+~~~
+hobo
+rooA
+Pele
+~~~
+**Input 2**
+~~~
+hobo
+Pele
+~~~
+
+**command**
+~~~
+python /Users/filipwierzbicki/Documents/PhD_Project/Bioinformatics/manna-code/cluster-msa.py --gap 0.09 --mm 0.1 --match 0.2 --input-format toy --clusters "1,2" --sample-IDs "1,2"|grep -v '^#'|awk '{print $1,$4}'
+~~~
+
+**output**
+~~~
+hobo hobo
+rooA -
+Pele Pele
+~~~




+
+

Toy examples modified by Filip Wierzbicki

Filip Wierzbicki — Mon, 28 Dec 2020 15:02:04 -0000

--- v3
+++ v4
@@ -1,48 +1,34 @@
 #Introduction
 Here, we demonstrate the performance of Manna using toy examples of different evolutionary scenarios.
-All alignments were run with the the following parameters: '--gap 0.09 --mm 0.1 --match 0.2 --input-format toy'

 The examples are shown without the output header. Furthermore, the default length and divergence values were ignored. 

-#Insertion
-Alignment between two related sequences of transposable element annotations are shown. The first input sequence carries an insertion of copia which is absent from the second input sequence.
-Input 1
+#Match
+Alignment between two identical sequences of transposable element annotations.
+**Input 1**
 ~~~
 hobo
-P-element
-gypsy
-I-element
-copia
-ZAM
-F-element
-X-element
-gtwin
+P-ele
+~~~
+**Input 2**
+~~~
+hobo
+Pele
 ~~~

-Input 2
+**command**
 ~~~
-hobo
-P-element
-gypsy
-I-element
-ZAM
-F-element
-X-element
-gtwin
+python /Users/filipwierzbicki/Documents/PhD_Project/Bioinformatics/manna-code/cluster-msa.py --gap 0.09 --mm 0.1 --match 0.2 --input-format toy --clusters "1,2" --sample-IDs "1,2"|grep -v '^#'|awk '{print $1,$4}'
 ~~~

-Output
+**output**
 ~~~
 hobo hobo
-P-element P-element
-gypsy gypsy
-I-element I-element
-copia -
-ZAM ZAM
-F-element F-element
-X-element X-element
-gtwin gtwin
+Pele Pele
 ~~~



+
+
+

Toy examples modified by Filip Wierzbicki

Filip Wierzbicki — Mon, 28 Dec 2020 14:46:44 -0000

--- v2
+++ v3
@@ -6,7 +6,7 @@

 #Insertion
 Alignment between two related sequences of transposable element annotations are shown. The first input sequence carries an insertion of copia which is absent from the second input sequence.
-###Input 1
+Input 1
 ~~~
 hobo
 P-element
@@ -19,7 +19,7 @@
 gtwin
 ~~~

-###Input 2
+Input 2
 ~~~
 hobo
 P-element
@@ -31,7 +31,7 @@
 gtwin
 ~~~

-###Output
+Output
 ~~~
 hobo hobo
 P-element P-element

Toy examples modified by Filip Wierzbicki

Filip Wierzbicki — Mon, 28 Dec 2020 14:35:07 -0000

--- v1
+++ v2
@@ -3,8 +3,8 @@
 All alignments were run with the the following parameters: '--gap 0.09 --mm 0.1 --match 0.2 --input-format toy'

 The examples are shown without the output header. Furthermore, the default length and divergence values were ignored. 
-#Examples
-##Insertion
+
+#Insertion
 Alignment between two related sequences of transposable element annotations are shown. The first input sequence carries an insertion of copia which is absent from the second input sequence.
 ###Input 1
 ~~~

Toy examples modified by Filip Wierzbicki

Filip Wierzbicki — Mon, 28 Dec 2020 14:34:38 -0000

Introduction

Here, we demonstrate the performance of Manna using toy examples of different evolutionary scenarios.
All alignments were run with the the following parameters: '--gap 0.09 --mm 0.1 --match 0.2 --input-format toy'

The examples are shown without the output header. Furthermore, the default length and divergence values were ignored.

Examples

Insertion

Alignment between two related sequences of transposable element annotations are shown. The first input sequence carries an insertion of copia which is absent from the second input sequence.

Input 1

hobo
P-element
gypsy
I-element
copia
ZAM
F-element
X-element
gtwin

Input 2

hobo
P-element
gypsy
I-element
ZAM
F-element
X-element
gtwin

Output

hobo hobo
P-element P-element
gypsy gypsy
I-element I-element
copia -
ZAM ZAM
F-element F-element
X-element X-element
gtwin gtwin