SecReT6
T6SS-Comp
It performs the MultiGeneBlast-facilitated gene cluster detection in user-defined search database based on sequence similarity and gene order.
Updated: 24-Nov-2013.       Recommended Browsers: Mozilla Firefox, Google Chrome.
Retrieve results

(i) One query sequence
        
         Example: Edwardsiella tarda PPD130/91 Type VI Secretion System T6SS [AY424360]
(1) or Select a completely sequenced bacterial genome from NCBI genome database
        
         Example: Escherichia coli O157:H7 str. EDL933 [NC_002655]
(2) Define the region (< 300 Kb) under analysis
        
      (3) Define the region (<300 Kb) under analysis within the uploaded sequence
        
How to prepare your complete or approximate complete sequence of a given bacterial genome as reference?
Easy to prepare the assembled contig/scaffold sequences from your partially sequenced bacterial genomes:
(1) Prepare a plain file containing the assembled contig/scaffold nucleotide sequences in the Multi-FASTA format, like mysequence.fas (3.9 Mb).
(2) Use CDSeasy to annotate your sequences.
  Upload your file, myseq.fas, into CDSeasy to generate a GenBank file, like, mysequence_.gbk;
  It takes ~10 minutes for CDSeasy to annotate the 5.3-Mb chromosomal sequence of K. pneumoniae strain HS11286.
(3) Upload your sequences as "Query sequence " of T6SS-Comp.
  Select the 'Genome Seq' tab then click the radio "or (1) Upload a GenBank file containing the nucleotide sequence and annotation");
  Upload the file CDSeasy-output file, myseq_.gbk.
or *(4) Upload your sequences as "Subject sequence set" of T6SS-Comp.
  Select the 'Upload sequence (1-5)';
  Upload the file CDSeasy-output file, mysequence_.gbk;

For partially sequenced bacterial genomes, CDSeasy firstly 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 sequence and annotation files in commonly used formats, such as GenBank.
(ii) Subject sequence set
(User could submit up to 50 bacterial sequences per job, including 1-5 via the 'Select genomes' tap, 1-40 via the 'Input acc. no' tap and/or 1-5 via the 'Upload sequences' tap)
(1) Enter the NCBI Refseq Genome accession no. separated by "return" (UPPER/lower case sensitive). [Format?] [Example]
or (2) No. of genomes from NCBI being compared with the query sequence? Example: select '2'
or (3) No. of sequences manually uploaded being compared with the query sequence?
How to prepare the user's genome data?
Run with Default options
(iii) BLAST parameters (Optional)
     (1) Number of Blast hits per gene to be mapped < (1~500)
     (2) Minimal sequence coverage of BLAST hits > (0~100) %
     (3) Minimal % identity of BLAST hits > (0~100) %
     (4) Maximum distance between genes in locus < (0~100) Kb
     (5) Weight of synteny conservation in hit sorting = (0~2.0)
(iv) Results retrieval options
Retrieve results
T6SS-Comp
Type in the Job_ID