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Predicting protein functional association in microbial and viral genomes by analysis of conservation of genomic context (Flanking Genes)

Functional associations of proteins can be predicted by conservation of the genomic neighbourhood surrounding the gene encoding the protein of interest. Our tool FlaGs clusters neighbourhood-encoded proteins into homologous groups and outputs the identity of the groups, a graphical visualization of the gene neighbourhood and its conservation, and optionally, a phylogenetic tree annotated with flanking gene conservation.


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For creating an input file for FlaGs from the results of an online BlastP or PSI-Blast search at the NCBI, you can use this guideline.

You can also use our reduced BLAST database to create larger input files for local FlaGs (up to 1000 sequences) using this form.


Paste your query in the box below:

Input can be one of the following (the format will be autodetected):

- A list of NCBI protein accessions (without any other characters such as tabs)*  

- A list of NCBI assembly numbers with associated protein accessions (tab separated)  

- A single protein sequence or NCBI accession**  

* these should be RefSeq accessions, but if they are not, FlaGs will try to find a RefSeq accession with an identical sequence

** In the case of a single sequence or accession, BlastP will be run to find more homologues in the RefSeq database. BlastP parameters can be changed below.



Or, upload query:



Your email address* (results will be sent here): 

Project title (eg. MyProject1): 

E-value (Default 1e-10): 

Number of jackhmmer iterations (Default 3): 

Number of flanking genes (Default 4): 


Optional BLASTP parameters if submitting a single sequence or accession:

Select Blast DB:

Updated on January 29, 2021

NCBI RefSeq Database (Excluding Eukaryotes)

Representative database (Click here for the list of genomes)

BlastP E-value (Default 1e-3): 

Number of hits returned (Default 15, max 100): 


Output Type:

With phylogenetic tree and query showed as tree order (input accessions should be homologous)
With phylogenetic tree but query showed as input order (input accessions should be homologous)
No phylogenetic tree and query showed as input order




You can download FlaGs to run locally from here.



FlaGs was first made by Chayan Kumar Saha and Gemma C. Atkinson. It is now developed by the Atkinson FlaGs team Jose Nakamoto, Artem Egorov and Veda Bojar at the Department of Experimental Medical Science, Lund University, Sweden. If you use FlaGs in your work, please cite our paper here.