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Longest gene search tool

Summary

Tool for finding list of gene-like sequences of max common length for given input list of sequences (aligned contigs). Input is in FASTA format, output is in FASTA-2 format.

Requirements

  • Python 3.6+
  • BioPython 1.71+

Parameters

  • -i, --input-file: input FASTA file with aligned contigs.
  • -o, --output-file: path to output FASTA-2 file.
  • -ms, --min-similarity: Minimal allowed similarity of sequences, in [0, 1] interval. By default is 0.95.

Example

python3 ./longest_gene.py -i examples/gregalis.fa -o output.fa