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 CGCfinder.
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 CGCfinder.
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.
The CDSeasy-generated GenBank file can be used directly as the input for VRprofile, CGCfinder and COGviewer.