This program requires as input a file containing protein or DNA sequences. These input files must be in FASTA format. The format is very simple. Every entry consists of a sequence identifier (ID), an optional comment (COMMENT), and a sequence (SEQUENCE). The format looks like this:
>ID COMMENT SEQUENCE
The special character ">" marks the beginning of a new sequence. The ">" character is followed immediately by the sequence identifier. The rest of that line is occupied by the optional comment. Subsequent lines contain the sequence itself.
Some rules about representing sequences:
Two alphabets are allowed. The protein alphabet contains twenty characters for amino acids ("ACDEFGHIKLMNPQRSTVWY") plus four more ambiguous characters ("BUXZ"). Here is a summary:
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 any
G glycine V valine
H histidine W tryptophan
I isoleucine Y tyrosine
K lysine Z glutamate or glutamine
L leucine X any
M methionine
N asparagine
The four-character DNA alphabet ("ACGT") is augmented by eleven
ambiguous characters, as follows:
A --> adenosine M --> A C (amino)
C --> cytidine S --> G C (strong)
G --> guanine W --> A T (weak)
T --> thymidine B --> G T C
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)
Here is an example of three sequences in FASTA format:
>ICYA_MANSE GDIFYPGYCPDVKPVNDFDLSAFAGAWHEIAKLPLENENQGKCTIAEYKY DGKKASVYNSFVSNGVKEYMEGDLEIAPDAKYTKQGKYVMTFKFGQRVVN LVPWVLATDYKNYAINYNCDYHPDKKAHSIHAWILSKSKVLEGNTKEVVD NVLKTFSHLIDASKFISNDFSEAACQYSTTYSLTGPDRH >LACB_BOVIN MKCLLLALALTCGAQALIVTQTMKGLDIQKVAGTWYSLAMAASDISLLDA QSAPLRVYVEELKPTPEGDLEILLQKWENGECAQKKIIAEKTKIPAVFKI DALNENKVLVLDTDYKKYLLFCMENSAEPEQSLACQCLVRTPEVDDEALE KFDKALKALPMHIRLSFNPTQLEEQCHI >BBP_PIEBR NVYHDGACPEVKPVDNFDWSNYHGKWWEVAKYPNSVEKYGKCGWAEYTPE GKSVKVSNYHVIHGKEYFIEGTAYPVGDSKIGKIYHKLTYGGVTKENVFN VLSTDNKNYIIGYYCKYDEDKKGHQDFVWVLSRSKVLTGEAKTAVENYLI GSPVVDSQKLVYSDFSEAACKVN