Toos:

• Search similar sequence using NCBI blast
• Combine multiple fasta files into one
• Multiple sequence alignment and visualization
• Visualize part of the aligned sequences
• Cluster aligned sequences based on similarity
• Analyze differences of two aligned sequences

Multiple sequence alignment and visualization (Informatics)

Take multiple sequences and align them with visual output.

Input

seq_fasta - file path to a single fasta file containing multiple sequences to be aligned reorder - whether the sequences should be reordered based on the similarity after alignment. Default to False

Output

• An image showing the aligned sequences, which are highlighted by amino acid similarity.
• Aligned sequences in the fasta format
• A pickle file containing the alignment object, the labels and the newick representation of the alignment tree, which can be used by other tools

Important! Please display the image in the response!

Cluster aligned sequences based on similarity (Informatics)

Using an intermediate result from a multiple sequence alignment, cluster the sequences based on their similarity and generate a dendrogram.

Input

intermediate_pkl_file - file path to the pickle file created from the "Multiple sequence alignment and visualization" tool

Output

• A dendrogram showing the clustering of the sequences

Analyze differences of two aligned sequences (Informatics)

Give a written summary of the differences between two aligned sequences. In the first part, sequences are aligned and gaps are indicated by dashes. Different residues are represented by lower-case letters. In the second part, all different residues are enumerated. You should use the full names of the amino acids to explain the differences.

Input

intermediate_pkl_file - file path to the pickle file created from the "Multiple sequence alignment and visualization" tool. The alignment object should contain exactly two sequences.

Output

The differences in the amino acid sequences between the two aligned sequences.

Setup

requirements

biotite matplotlib numpy