GeneSweep

Sweep reference genes across hundreds of genomes at once: presence, identity, coverage and mutations. Everything runs in your browser, no files are uploaded anywhere.

1. Reference gene(s), FASTA

2. Genome files (select many, .fasta .fa .fna, .gz works)

3. Genome order list (optional, .txt)

One exact genome file name per line, with extension (for example isolate_01.fasta). Results, CSV and FASTA will follow this order. Files not in the list go last. Names in the list with no uploaded file appear as Missing.

Min identity %

Min coverage %

Max E-value

Keep only isolates found in all reference genes (applies to the FASTA files) Maximize matches (relaxed search down to 60% identity, slower) Reference is a coding sequence (classify point mutations as synonymous, missense or nonsense, and indels as frameshift or in-frame)

Advanced scoring and seed settings

Match score

Mismatch score

Gap penalty

Seed length (6-12)

Two-hit window

X-drop

Min ungapped score

Match must be positive, mismatch and gap negative. Shorter seeds find more distant genes but run slower.
X-drop: how far the score may fall below its best value before an extension stops. Higher tolerates longer bad stretches but is slower.
Min ungapped score: the score a gap-free stretch needs to be kept for full alignment. Lower is more sensitive but gives more false leads.

Genome	Gene	Status	Identity %	Coverage %	Contig	Start	End	Strand	Copies	Bitscore	E-value	Variants	Truncation