FlaGs3

Conserved gene neighbourhoods around your proteins of interest.

Give FlaGs3 a list of protein accessions. For each one it fetches the genome, cuts out the flanking genes, clusters all flanking proteins into homologous families with jackhmmer, and draws the neighbourhoods side by side with families in matching colours, so that conserved gene context stands out. Optionally it builds a phylogenetic tree of the query proteins and annotates Pfam domains on every flanking protein. Results stay on the server for 5 days and can be downloaded as one archive.

This is the FlaGs3 web service; the command-line tool with all its options is on GitHub. The previous version runs as webFlaGs.

Query proteins

One query per line: a protein accession, or a protein accession and its assembly separated by whitespace. Up to 200 queries per job. Load the demo list.

The file replaces the text box when both are given.
Neighbourhood and clustering
Extras
mafft, trimAl and VeryFastTree; adds minutes for large lists.
Run
Passed to NCBI with every request, as their Entrez service requires. Nothing is sent to it.
Names the result archive.
Input format

Each line is one query. A bare accession is looked up at NCBI, which finds the genome it comes from; a pair PROTEIN<tab>ASSEMBLY names the genome directly and skips the lookup. Lines starting with # are ignored. Three kinds of genome are understood:

  • NCBI: RefSeq or GenBank proteins (WP_…, NP_…, YP_…, AAC…) and assemblies (GCF_…, GCA_…). A bare accession is enough.
  • ENA: the protein as it is named in the ENA record, paired with a sequence accession (U00096, CP003200.1) or a WGS set (CABHOY01). Always a pair.
  • MGnify: a MAG locus tag paired with its catalogue accession (MGYG000454827_00001<tab>MGYG000454827). Always a pair.

Queries that cannot be resolved or whose genome cannot be fetched are listed in the run summary and the job still completes for the rest.