Kielce, Poland 2007

gp2fasta

gp2fasta is converting gp files from NCBI GenPept or GenBank format to fasta. Its main purpose is to create fasta files with short, but still accurate headers for sequence.

For example:
>Strpur-115729834-h
PNQILMQFRLDDNGSSYYKELASIIYGASPEFELAIFTVCFKENPNALSTFTMAGGITQKVQTWDYNGGYIGSAYFSV

stands for:
gi: 115729834
organism: Strongylocentrotus purpuratus
additional: h (hypothetical protein)
sequence:PNQILMQFRLDDNGSSYYKELASIIYGASPEFELAIFTVCFKENPNALSTFTMAGGITQKVQTWDYNGGYIGSAYFSV

Options:
- for id: GI or LOCUS;
- for organism: e.g. Mus musculus, M.musculeu or Musmus;
- detailed definition;
- additional information:
    P -> PREDICTED
    s -> similar
    h -> hypothetical protein
    u -> unnamed protein product
    n -> novel
    p -> putative
    o -> open reading frame

Each option is separated with "separator" (in this case "-").

Example file

Free QT4 version of gp2fasta with GUI

Other links:
Protein isoelectric point calculator