[maker-devel] *maker.proteins and *non_overlapping_ab_initio.proteins files

[Carson Holt]

 1. by view the gff file produced by maker2, I have found most of the
predicted gene loci have est matches. but why only 254 gene annotations got
by maker2 ?

>> I'd really have to see the results to tell you why.


2. in the ³non-overlapping ab initio²file, I found sequences are all from
augustus_masked prediction. Does the non-overlapping file only include the
best gene modes from predicted by both augustus and genemark?  Does it
include genemark- or augustus-specific genes ?
 
>> The "non-overlapping" file should have the one with best consensus if there
>> are 3 or more predictors, and the longest one otherwise.  It should be able
>> to have augustus and genemark genes.  Try it with only genemark and let me
>> know if the file is empty.

Thanks,
Carson




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