T6SS prediction detects T6SS gene clusters in an annotated or unannotated genome sequence by BLASTp 2.10.1+ or hmmsearch (HMMER v3.3.1) against experimentally validated T6SSs recorded in SecReT6.
(1) If your genome sequence is unannotated, you can paste a nucleotide sequence of your genome or upload FASTA format file and run the prediction. In this case, gene-finding tool Prodigal v2.6.3 is first utilized to annotate the sequence before detection of T6SS gene clusters using BLASTp 2.10.1+ or hmmsearch (HMMER v3.3.1).
(2) If your genome sequence is already annotated, you can upload GenBank file (GenBank file example) containing both annotations and genome sequence. In this case, DNA sequences of annotated genes would be extracted and translated as queries for BLASTp 2.10.1+ or hmmsearch (HMMER v3.3.1).