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      Motivated by the concept of Chou's pseudo amino acid composition, the pseudo k-tuple nucleotide composition (PseKNC) was proposed to represent DNA sequences and the server PseKNC was designed in a flexible way, allowing users to generate various kinds of pseudo nucleic acid composition for a given DNA sequence by selecting different parameters and their combinations.

(1) What's the difference of "Type 1" and "Type 2" PseKNC ?
     Type 1 PseKNC, which is also called parallel-correlation type and generates (4k+λ)-D vector for each DNA sequence; Type 2 is also called the series-correlation type and generates (4k+l*λ)-D vector, where l is the number of physicochemical property attributes selected.
     For detailed information, please click the “?” symbol after “PseKNC mode”.

(2) What's the weight factor ?
      The weight factor is designed for the users to put weight to the addional PseKNC with respect to the conventional nucleic acid components. The users are allowed to select the weight factor from 0.1 to 1.0. For detailed information, please click the “?” symbol after weight factor.

(3) What's the λ factor?
      The counted rank (or tier) of the correlation along a DNA sequence is usually represented by λ. In Type 1 PseKNC, the user will obtain (4k+λ)-D vector for each sequence; in Type 2 PseKNC, (4k+l*λ)-D vector is generated, (where l is the number of physicochemical property attributes selected). It's also important to note that λ should be smaller than L-k, where L is the length of the query sequence and k is the length of the selected oligonucleotide mode (Dinucleotide model k=2 and Trinucleotide model k=3). If the user choose λ=0, then the output will be the conventional 4k-D nucleic acid composition for both cases. For detailed information, please click the “?” symbol after lambda.

(4) What's the input format?
      The user must input the DNA sequences in FASTA format, i.e., each DNA sequence should start with a greater-than symbol (" > ") in the first column. The words right after the " > " symbol in the single initial line are optional and only used for the purpose of identification and description. Currently, PseKNC accepts maximum 500 DNA sequences for each submission.

(5) How to use it?
Step 1 Select the PseKNC mode, Type1 or Type 2;
Step 2 Select the PseKNC k-tuple, Dinucleotide or Trinucleotide;
Step 3 Select the corresponding phychemical property;
Step 4 Select the weight factor and λ;
Step 5 Enter the query DNA sequences in fasta format and then click the submit button.

 

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