TAfinder - a blast based tool for recognition of type II toxin-antitoxin system

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Input Your Sequence

1. Paste a Pair of Gene/Protein Sequence (FASTA format)

The coordinate in genome of your First sequence is ..

The coordinate in genome of your Second sequence is ..

If the coordinates of your input sequences are not available, please set the first residue in your first sequence as 1st, calculate and fill the rest.
Example : seq1: 1..396 , seq2: 398..694

Or 2. Select a Completely Sequenced Bacterial Genome from here

Example: Escherichia coli ED1a chromosome [NC_011745]

Or 3. Enter a Refseq Accession Number

Example: NC_011745

Or 4. Upload Your Sequence

4.1 Upload an Annotated Genome Sequence

Please:

Upload an FAA File (Required) Example: Example.faa
Upload a PTT File (Required) Example: Example.ptt
Or if you don't have FAA file or PTT file, you can upload the corresponding GenBank File to Generate the File Required Example: Example2.gb with CDS translated sequence

Instruction:

We Need Both an FAA file and a PTT file.

The GenBank (full) file with protein sequences such as Example2.gb can be used to generate BOTH of these two files (FAA and PTT).
BUT the GenBank file without translated sequence such as Example_error.gb can only generate the PTT file but not the FAA file.

or 4.2 Upload an unannotated complete genome sequence

Example: Example.fas

Instruction: Please use CDSeasy to quick annotate your complete sequence [with the "CDSeasy includes" option of "ONLY Gene finding (Prodigal)"],
and then submit the generated .gbk file into the above section "4.1 Upload an Annotated Genome Sequence".

or 4.3 Upload the unannotated Contig/Scaffold sequences

Example: Example.fas

Instruction: Please use CDSeasy to quick annotate your Contig/Scaffold sequences [with the "CDSeasy includes" option of "ONLY Gene finding (Prodigal)"],
and then submit the generated .gbk file into the above section "4.1 Upload an Annotated Genome Sequence".

Set Parameters (Optional)

(1) E-value for BLAST = (0.000001~0.01)

(2) E-value for HMMer = (0.001~1)

(3) Maximum length of potential toxin/antitoxin = (30~500 aa)

(4) Maximum distance(or overlap) between potential toxin and antitoxin = (-50~300 nt) (overlap_gap nt, in this case, it means gap between 20 nt overlap and 150 nt. )

Please click "Run" after the required file has been uploaded.