Shawn Rynearson

Hello I'm having a bit of an issue with the sbt test section of the tutorial. From the spark-scala-tutorial root directory: ``` {}~/spark-scala-tutorial sbt Java HotSpot(TM) 64-Bit Server VM warning:...

Request "fingerprint contig", to go with FPCmap (SO:0001250)

3

An FPCmap (SO:0001250) is often composed of several fingerprinted contigs (FPC). Currently there is no term for FPC. More info: The individual contigs are composed of several BACs (SO:0000153). The...

move oligo_U_tail and polyA_sequence [sf#156]

5

**Reported by batchelorc on 2009-07-30 13:59 UTC** Just to check whether this is OK: (1) polyA_sequence is_a mRNA_region (2) oligo_U_tail is_a guide_RNA_region best wishes, Colin.

inconsistency: "TF_binding_site" or "DNA_motif" as parent [sf#209]

4

**Reported by kchris on 2010-06-12 00:00 UTC** Hi, There are some promoter motifs, e.g. the "A_box" that is part_of "RNApol_III_promoter_type_2" that are is_a children of "TF_binding_site", which is a descendent...

repeat_fragment [sf#210]

6

**Reported by scalabrin on 2010-06-22 13:06 UTC** Dear curator, I checked the documentation and the mailing list, in particular this: http://sourceforge.net/tracker/index.php?func=detail&aid=1720110&group\_id=72703&atid=810408 but I am still unable to write gff3 files...

**Reported by batchelorc on 2010-11-26 10:02 UTC** Hello, There's active discussion on the obi-devel list of SO's "genotype" definition. This term request is a placeholder till we find out what's...

**Reported by eilbeck on 2011-03-03 17:57 UTC** Message from Jim Hu: What SO term do I use for the cistrons in a polycistronic transcript? CDS doesn't seem right for cases...

missense mutation [sf#295]

1

**Reported by pgaudet on 2012-01-18 16:34 UTC** Hello, There are a few issues concerning missense mutations: 1. SO:0001583 : non-synonymous_codon should have as part of its definition 'non-sense mutation' (or...

Transposon_CDS/Transposon_pseudogene [sf#299]

1

**Reported by davpabenwo on 2012-02-20 12:19 UTC** To allow for the classification of a non-genomic coding/pseudogenic gene structure. I guess these would have to be child terms of CDS and...

Hi Folks I am working with synthetic promoter constructs. So each of these consists of an upstream region that binds a transcription factor that either activates or represses transcription. Then...