Sequence Manipulation

These tools were created to assist with various sequence manipulations that you might find helpful as pre-processing steps before running the RNA2DMut tool on your sequence.

Sequential Insertion

Sequential_Insertion takes a string (e.g. biological sequence data like RNA/DNA/Protein) and adds insertions

The input_sequence is whatever sequence you wish to manipulate. It must be a continuous string with no linebreaks.
The step_size defines the steps to take in making the serial "mutations" to the sequence: e.g. a value of  will make a change every 5 characters (nts)
The indel_input defines what change to make. When indel_input is a string of characters (e.g. nts) that string is inserted at the step.
The output is in Fasta format where a title is given. The first sequence is the input_sequence, all mutants follow where the change is defined.

Sequence Deletion

Sequence_Deletion takes a string (e.g. biological sequence data like RNA/DNA/Protein) and makes deletion mutations.

Here, the input_sequence is whatever sequence you wish to manipulate. It must be a continuous string with no linebreaks.
The step_size defines the steps to take in making the serial "mutations" to the sequence: e.g. a value of  will make a change every 5 characters (nts)
The indel_input defines what change to make. Numerical data (an integer value) will delete that number of residues from the sequence at every step.
The output is in Fasta format where a title is given. The first sequence is the input_sequence, all mutants follow where the change is defined.

Sequential Substitution

Sequential_Substitution takes a string (e.g. biological sequence data like RNA/DNA/Protein) and sequentially substitutes a sequence fragment.

Here, the input_sequence is whatever sequence you wish to manipulate. It must be a continuous string with no linebreaks.
The step_size defines the steps to take in making the serial "mutations" to the sequence: e.g. a value of 5 will make a change every 5 characters (nts)
The substituted_sequence defines what sequence to substitute at each position.
The output is in Fasta format where a title is given. The first sequence is the input_sequence, all mutants follow where the change is defined.

Sequence Reverse Complement

Sequence_Reverse_Complement is a program for reverse complementing nt sequence data.

Sequence Scramble

Sequence_Scramble is a program for scrambling biological sequence data.