shin-kinos / seq-weighting

Give weighting scores to each AA sequences in MSA.

seq-weighting

Description

• A program that calculates sequence weighting in Multiple Sequence Alignment.
• It supports two types of weighting, position-based method[1] and distance-based method[2].

Compilation

You can compile the program with Cargo. 🦀📦

[e.g.]

% cd seq-weighting-main
% cargo build --release

Then the object file will be generated in ./target/release directory.

Input file format

Aligned Multi-FASTA format in amino acid sequences.
See sample files in demo directory.

Usage

• -i : Input file name, REQUIRED.
• -o : Output file name, REQUIRED.
• -m : Method of weighting, position-based or distance-based.

[e.g.]

% ./seq-weighting -i input.fasta -o output.txt -m va 

Type -h to see other available options.

Output

[e.g.]

References

1. Henikoff, Steven, and Jorja G. Henikoff. "Position-based sequence weights." Journal of molecular biology 243.4 (1994): 574-578.
2. Vingron, Martin, and Patrick Argos. "A fast and sensitive multiple sequence alignment algorithm." Bioinformatics 5.2 (1989): 115-121.