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:
s >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

My other projects:

Proteome-pI 2.0 - Proteome Isoelectric Point Database 2.0 - predicted isoelectric point for ~61 million proteins accross 20,115 organisms
IPC 2.0 - prediction of isoelectric point and pKa dissociation constants
Isoelectric Point Calculator - isoelectric point and molecular weight from protein sequence
Proteome-pI - Proteome Isoelectric Point Database - predicted isoelectric point for ~21 million proteins accross 5,029 organisms
GDFuzz3D - protein contact map to 3D structure retrieval service
MetaDisorder - Prediction of Intrinsically Unstructured Proteins (protein disorder) from amino acid sequence only
CompaRNA - continuous benchmarking of RNA structure prediction methods
Shannon entropy calculator - Real example how to calculate and interpret information entropy
fCite - a tool to quantify an individual's scientific research output based on citations, RCR, and the H-index divided by the number of authors in publications (the system integrates the data from over 33 million publications with half-billion citations and references for over 1 million ORCID users)

Personal site of the author