[maker-devel] gff file: possible sources

[Daniel Ence]

Hi Qihua, the cdna2genome is the polished tblastx alignments from Exonerate. Basically, the source column should be the name of the tool that generated the alignment, prediction, or gene model.

~Daniel


Daniel Ence
Graduate Student
Eccles Institute of Human Genetics
University of Utah
15 North 2030 East, Room 2100
Salt Lake City, UT 84112-5330

On Jan 11, 2017, at 11:28 PM, Qihua Liang <qlian003 at ucr.edu<mailto:qlian003 at ucr.edu>> wrote:

Hi Maker develop team!

I am trying to figure the second column of gff file generated by maker, which should be the source of this annotation. Besides of what the tutorial lists as,

Possible Sources Include:

  *   BLASTN - BLASTN alignment of EST evidence
  *   BLASTX - BLASTX alignment of protein evidence
  *   TBLASTX - TBLASTX alignment of EST evidence from closely related organisms
  *   EST2Genome - Polished EST alignment from Exonerate
  *   Protein2Genome - Polished protein alignment from Exonerate
  *   SNAP - SNAP ab inito gene prediction
  *   GENEMARK - GeneMarkab inito gene prediction
  *   Augustus - Augustus ab inito gene prediction
  *   FgenesH - FGENESH ab inito gene prediction
  *   Repeatmasker - RepeatMasker identified repeat
  *   RepeatRunner - RepeatRunner identified repeat from the repeat protein database
  *   tRNAScan - tRNAScan-SE tRNA predictions (coming soon)
  *   PASA - PASA gene predictions (coming soon)

There are other sources that I noticed from my gff file, like cdna2genome. Is there any other detailed documentation explaining such sources besides of those listed above?

Thanks
Qihua

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