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DNAM/PECAAN GeneMark calls differ?

| posted 19 Feb, 2017 16:56
On occasion, when I compare called start sites between DNA Master and PECAAN, I see different results. For example, with Royals2015, in DNA Master I see "Original Glimmer call @bp 36409 has strength 8.82" but in PECAAN I see "Glimmer Start: 36409 Glimmer Score: 8.82 GeneMark Start: 36352 Starterator Start: Pham 24601". I have seen this other times, where PECAAN states different starts for GL and GM, but DNAM gives only one start (implying GM and GL agree).

Have others noticed this? Anyone have an explanation?

| posted 19 Feb, 2017 20:55
I am pretty sure that this is simply due to two independent autoannotations differing in some calls. If you have a class of students each run the autoannotation independently, you will find cases of this where the calls are slightly different in some cases.

| posted 25 Jan, 2018 15:57
We are seeing this too - which leads me to this question.
For annotation of Gordiona phages in PECAAN, is there a preference to which GENEMARK file is uploaded to PECAAN and hence will ultimately be incorporated in the DNA MASTER file.

We used Gordonia bronchialis as our host for the GENEMARK input for PECAAN and are now wondering if GENEMARK S is a better option. Which one does DNAM use as a default?

Edited 25 Jan, 2018 15:58
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