Java code

Mfind, which is a Java implementation for the iterative comparison of genetic sequences (script is available in a file named Mfind_script.txt). It performs an exhaustive search of n-size conserved subsequences within a set of sequences. Mfind operates on a multi-FASTA file, where the first sequence in the set is considered the problem sequence (PS). It then employs a parallel sliding window technique to search for variability. The sliding window is a problem-solving technique of data structure and algorithm for problems that apply arrays or lists

Dataset

The result was a folder containing the following: (1) A text file named metadata with the reference information from angiosperm barcodes around the world, registered at that moment; (2) a text file named fasta.fas containing the DNA barcodes which includes COI, rbcL, matK, trnL-F, trnH-psbA, ITS among other genes registered in FASTA format.

Cite: Ríos-Willars, E., Chirinos-Arias, M. C. (2024). Mfind: A tool for DNA barcode analysis in angiosperms and its relationship with microsatellites using a sliding window algorithm. Planta 259, 134 https://doi.org/10.1007/s00425-024-04420-3. Link