FTGPRED: Gene Identification using Fourier Transformation

Help and Features of FTGPRED
  1. Paste or Submit Your Sequence:

    The DNA sequence can be pasted into the text area. Or a file containing nucleotide sequence can be uploaded using this option.

  2. Select Region for Analysis:

    Users can select a particular region from the input sequence data for similarity search. This option saves the user the job of continuously trimming and editing their sequence in case they want to restrict their search to a particular region.

  3. Specify Input Format of Your Sequence:

    In case the Format of the sequence is any of the standard ones (EMBL, FASTA, GENBANK, etc.) then `Format Type' should be selected to `Standard Format (Readable by READSEQ)'. The FTGPRED server uses READSEQ program developed by D.G. Gilbert Indiana University to convert the format of your sequence to fasta. In case the input sequence is just plain text, set the `Format Type' to Plain Text (Single Letter Code). By default the server takes only single letter code of amino acids or nucleotide bases. The server will read the three letter code of amino acids as three different residues. The server also has the capability to ignore all the non-standard characters such as ,*%!@$% etc.

  4. Graphical View of Results

    The graphical output provides the user with a GIF image generated by the server. It depicts through a diagram, the approximate location of the detected ORF in the user-input sequence. Additional Information like the compositional analysis, including single nucleotide counts and GC dinucleotide counts of both ORF and the user-input sequence is provided for the benefit of the user. An example is shown below.

    Example for graphical output

    The graphical output for the spectrum can also be viewed. A GIF image of the spectrum is generated by the server plotting the graph of frequency vs Power. The power of spectrum at frequency f=1/3 is calculated and presented on the figure. Other mundane information are also provided to the user.

    Example for spectral output
  5. Minimum Size:

    FTGPRED requires you to input the minimum length of ORF you want to evaluate using Fourier Tansformation. However, a default value of 30 bp is taken by the server if no input is given.

  6. Start Codons:

    Three start codons are given as choices for the user. These are ATG, TTG and GTG. These start codons are taken from their frequency of occurence reported in literature.

  7. Fourier Transformation:

    Details regarding the basic FTG algorithm and other facts such as importance of FFT in biology can be obtained from this link.

  8. Email reply facility:

    Users wishing to to be intimated on completion of their job(s) can avail of this facility. The mail provides the user with the link to visit for evaluating the FTGPRED results and further analysis.

  9. Batch Processing facility:

    Users having more than one sequence to analyse can input their sequences through this option. However, the server accepts only formatted sequences with this option. At present no limit has been put to the number of sequences that can be submitted.

  10. Retrieval of results:

    Users can retrieve the results of their Job by providing the Job number that is given to the user on submission.

  11. Algorithm:

    FTG algorithm
    FTG algorithm
    FTG algorithm