TREP, the TRansposable Elements Platform

FASTA format description

(adapted from NCBI Documentation)

A sequence in FASTA format begins with a single-line description, followed by lines of sequence data. The description line is distinguished from the sequence data by a greater-than (">") symbol in the first column. It is recommended that all lines of text be shorter than 80 characters in length. An example sequence in FASTA format is:

>gi|532319|pir|TVFV2E|TVFV2E envelope protein
ELRLRYCAPAGFALLKCNDADYDGFKTNCSNVSVVHCTNLMNTTVTTGLLLNGSYSENRT
QIWQKHRTSNDSALILLNKHYNLTVTCKRPGNKTVLPVTIMAGLVFHSQKYNLRLRQAWC
HFPSNWKGAWKEVKEEIVNLPKERYRGTNDPKRIFFQRQWGDPETANLWFNCHGEFFYCK
MDWFLNYLNNLTVDADHNECKNTSGTKSGNKRAPGPCVQRTYVACHIRSVIIWLETISKK
TYAPPREGHLECTSTVTGMTVELNYIPKNRTNVTLSPQIESIWAAELDRYKLVEITPIGF
APTEVRRYTGGHERQKRVPFVXXXXXXXXXXXXXXXXXXXXXXVQSQHLLAGILQQQKNL
LAAVEAQQQMLKLTIWGVK

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  tryptophan
  I  isoleucine                      Y  tyrosine
  K  lysine                          Z  glutamate or glutamine
  L  leucine                         X  any
  M  methionine                      *  translation stop
  N  asparagine                      -  gap of indeterminate length

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