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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.
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<div class="">~Daniel</div>
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<div class="">Daniel Ence<br class="">
Graduate Student<br class="">
Eccles Institute of Human Genetics<br class="">
University of Utah<br class="">
15 North 2030 East, Room 2100<br class="">
Salt Lake City, UT 84112-5330 </div>
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<div class="">On Jan 11, 2017, at 11:28 PM, Qihua Liang <<a href="mailto:qlian003@ucr.edu" class="">qlian003@ucr.edu</a>> wrote:</div>
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Hi Maker develop team!
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<div class="">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,</div>
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Possible Sources Include:</div>
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<li style="margin-bottom: 0.1em;" class="">BLASTN - BLASTN alignment of EST evidence</li><li style="margin-bottom: 0.1em;" class="">BLASTX - BLASTX alignment of protein evidence</li><li style="margin-bottom: 0.1em;" class="">TBLASTX - TBLASTX alignment of EST evidence from closely related organisms</li><li style="margin-bottom: 0.1em;" class="">EST2Genome - Polished EST alignment from Exonerate</li><li style="margin-bottom: 0.1em;" class="">Protein2Genome - Polished protein alignment from Exonerate</li><li style="margin-bottom: 0.1em;" class="">SNAP - SNAP <i class="">ab inito</i> gene prediction</li><li style="margin-bottom: 0.1em;" class="">GENEMARK - GeneMark<i class="">ab inito</i> gene prediction</li><li style="margin-bottom: 0.1em;" class="">Augustus - Augustus <i class="">ab inito</i> gene prediction</li><li style="margin-bottom: 0.1em;" class="">FgenesH - FGENESH <i class="">ab inito</i> gene prediction</li><li style="margin-bottom: 0.1em;" class="">Repeatmasker - RepeatMasker identified repeat</li><li style="margin-bottom: 0.1em;" class="">RepeatRunner - RepeatRunner identified repeat from the repeat protein database</li><li style="margin-bottom: 0.1em;" class="">tRNAScan - tRNAScan-SE tRNA predictions (coming soon)</li><li style="margin-bottom: 0.1em;" class="">PASA - PASA gene predictions (coming soon)</li></ul>
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<div class="">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?</div>
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<div class="">Thanks</div>
<div class="">Qihua</div>
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