T-epitope Designer


		Input format A sequence in FASTA format begins with a single-line description, followed by lines of sequence data. The description line starts with a greater than symbol (">"). The word following the greater than symbol (">") immediately is the "ID" (name) of the sequence, the rest of the line is the description. The "ID" and the description are optional. All lines of text should be shorter than 80 characters. The sequence ends if there is another greater than symbol (">") symbol at the beginning of a line and another sequence begins. The following is an example: >Example1 envelope protein ELRLRYCAPAGFALLKCNDADYDGFKTNCSNVSVVHCTNLMNTTVTTGLLLN Sequences are expected to be represented in the standard IUB/IUPAC amino acid and nucleic acid codes, with these exceptions: lower-case letters are accepted and are mapped into upper-case; a single hyphen or dash can be used to represent a gap of indeterminate length; and in amino acid sequences, U and * are acceptable letters (see below). Before submitting a request, any numerical digits in the query sequence should either be removed or replaced by appropriate letter codes (e.g., N for unknown nucleic acid residue or X for unknown amino acid residue). The nucleic acid codes supported are: A --> adenosine M --> A C (amino) C --> cytidine S --> G C (strong) G --> guanine W --> A T (weak) T --> thymidine B --> G T C U --> uridine D --> G A T R --> G A (purine) H --> A C T Y --> T C (pyrimidine) V --> G C A K --> G T (keto) N --> A G C T (any) - gap of indeterminate length For those programs that use amino acid query sequences (BLASTP and TBLASTN), the accepted amino acid codes are: A alanine P proline B aspartate or asparagine Q glutamine C cystine R arginine D aspartate S serine E glutamate T threonine F phenylalanine U selenocysteine G glycine V valine H histidine W tryptophane I isoleucine Y tyrosine K lysine Z glutamate or glutamine L leucine X any M methionine * translation stop N asparagine - gap of indeterminate length * If you are trying to submit plain/raw sequence, make it FASTA by simply adding a first line consisting of a ">": > VHDDLEEEAADLLLVSSR