What it does

This tool converts data from a GenBank flat file format to GFF (scroll down for format description).

Example

• The following data in GenBank format:

  LOCUS       NM_001202705            2406 bp    mRNA    linear   PLN 28-MAY-2011
  DEFINITION  Arabidopsis thaliana thiamine biosynthesis protein ThiC (THIC)
              mRNA, complete cds.
  ACCESSION   NM_001202705
  VERSION     NM_001202705.1  GI:334184566.........
  FEATURES             Location/Qualifiers
       source          1..2406
                       /organism="Arabidopsis thaliana"
                       /mol_type="mRNA"
                       /db_xref="taxon:3702"........
       gene            1..2406
                       /gene="THIC"
                       /locus_tag="AT2G29630"
                       /gene_synonym="PY; PYRIMIDINE REQUIRING; T27A16.27;........
  ORIGIN
      1 aagcctttcg ctttaggctg cattgggccg tgacaatatt cagacgattc aggaggttcg
      61 ttcctttttt aaaggaccct aatcactctg agtaccactg actcactcag tgtgcgcgat
      121 tcatttcaaa aacgagccag cctcttcttc cttcgtctac tagatcagat ccaaagcttc
      181 ctcttccagc tatggctgct tcagtacact gtaccttgat gtccgtcgta tgcaacaaca
  //
  

• Will be converted to GFF3:

  NM_001202705    gbk2gff chromosome      1       2406    .       +       1       ID=NM_001202705;Alias=2;Dbxref=taxon:3702;Name=NM_001202705
  NM_001202705    gbk2gff gene    1       2406    .       +       1       ID=AT2G29630;Dbxref=GeneID:817513,TAIR:AT2G29630;Name=THIC
  NM_001202705    gbk2gff mRNA    192     2126    .       +       1       ID=AT2G29630.t01;Parent=AT2G29630
  NM_001202705    gbk2gff CDS     192     2126    .       +       1       ID=AT2G29630.p01;Parent=AT2G29630.t01
  NM_001202705    gbk2gff exon    192     2126    .       +       1       Parent=AT2G29630.t01
  

Reference

GBK-to-GFF is part of oqtans package and cited as [1].

About file formats

GenBank format An example of a GenBank record may be viewed here

GFF Generic Feature Format is a format for describing genes and other features associated with DNA, RNA and Protein sequences. GFF lines have nine tab-separated fields:

1. seqid - Must be a chromosome or scaffold or contig.
2. source - The program that generated this feature.
3. type - The name of this type of feature. Some examples of standard feature types are "gene", "CDS", "protein", "mRNA", and "exon".
4. start - The starting position of the feature in the sequence. The first base is numbered 1.
5. stop - The ending position of the feature (inclusive).
6. score - A score between 0 and 1000. If there is no score value, enter ".".
7. strand - Valid entries include '+', '-', or '.' (for don't know/care).
8. phase - If the feature is a coding exon, frame should be a number between 0-2 that represents the reading frame of the first base. If the feature is not a coding exon, the value should be '.'.
9. attributes - All lines with the same group are linked together into a single item.

Copyright

GBK-to-GFF Wrapper Version 0.6 (Apr 2015)

2009-2015 Max Planck Society, University of Tübingen & Memorial Sloan Kettering Cancer Center