Toy examples

Introduction

Here, we demonstrate the performance of Manna using toy examples of different evolutionary scenarios.

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

Match

Alignment between two identical sequences of transposable element annotations.

Input 1

hobo
Pele

Input 2

hobo
Pele

command

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

hobo hobo
Pele Pele

Insertion/deletion polymorphism

Alignment between two similar sequences of transposable element annotations with a presence/absence polymorphisms of a rooA in input 1.

Input 1

hobo
rooA
Pele

Input 2

hobo
Pele

command

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

hobo hobo
rooA -
Pele Pele

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

Shared polymorphism

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 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

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

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 

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 sequences with an insertion of "x" into "c" resulting in a fragmented annotation of "c" in input 1.

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