SecReT6


I. T6SS gene cluster detection and comparison

(1) T6SS-HMMER, identify the T6SS gene cluster by using HMM searches.

(2) T6SS-BLASTp, identify the T6SS gene cluster by using BLASTp searches.

(3) T6SS-Comp, compare T6SS gene clusters among the user-input multiple sequences. Tutorial

II. Effector/Immunity/Component protein searches

(5) WU-BLAST2 search against the T6SS components or effector/immunity proteins in SecReT6.

(4) HMMER3::phmmer search against the T6SS components or effector/immunity proteins in SecReT6.

(6) NCBI-BLASTp search against T6SS effector/immunity proteins in SecReT6.

(7) NCBI RPS-BLAST search against the conserved domains of T6SS core components in SecReT6.

III. Bacterial genome rapid annotation

(8) CDSeasy, protein-coding gene prediction for assembled contigs and initial functional annotation.

CDSeasy is designed for enhanced efficient annotation of assembled sequence contigs from a bacterial WGS project. It accepts assembled contig/scaffold sequences in multi-FASTA format or a complete genome sequence in FASTA format. For partially sequenced bacterial genomes, it generates a 'virtual complete genome' ('pseudochromosome') by connecting contig sequence without considering contig order and provides both contig-specific gene coordinates and corresponding pseudochromosome data. CDSeasy outputs include the protein-coding sequence and annotation files in commonly used formats, such as GenBank and NCBI PTT, to allow the contigs be visualized with a genome browser. The CDSeasy-generated GenBank file can be used directly as the input for other SecReT6 tools, such as T6SS-Comp.