Search found 6 matches

by bdanner
Fri May 11, 2012 8:28 pm
Forum: Annotation Questions
Topic: Help with first exon of CG10565 in Fosmid 18 of D. erecta
Replies: 2
Views: 4362

Re: Help with first exon of CG10565 in Fosmid 18 of D. erect

Thank you! The negative direction sequences always confuse me.
by bdanner
Wed May 09, 2012 8:33 pm
Forum: Annotation Questions
Topic: Help with first exon of CG10565 in Fosmid 18 of D. erecta
Replies: 2
Views: 4362

Help with first exon of CG10565 in Fosmid 18 of D. erecta

We are working with D. erecta Jan. 2008 (GEP/3L extended) Fosmid 18. We found that exon 1 of gene CG10565 (PB/PA) has in-frame stop codons in all reading frames except the third reading frame, but the methionines are way downstream of where BLAST calls the gene. We are not sure where the start of th...
by bdanner
Sat Mar 03, 2012 11:35 am
Forum: Annotation Questions
Topic: D. erecta fosmid39 grey and dark grey blast hits question
Replies: 2
Views: 4161

Re: D. erecta fosmid39 grey and dark grey blast hits questio

Makes sense! Thanks a bunch Wilson!
by bdanner
Wed Feb 29, 2012 10:15 pm
Forum: Annotation Questions
Topic: D. erecta fosmid39 grey and dark grey blast hits question
Replies: 2
Views: 4161

D. erecta fosmid39 grey and dark grey blast hits question

D. erecta fosmid39 Jan 2008. fosmid39.jpg We are unsure what it means to have BLAST hits that are dark grey and grey? On further research we found that CG17904-PA, CG3262-PD, CG34105-PA, and CG12491-PA are all on different chromosomes than 3L. Did this mean that these jumped and, if so, how should w...
by bdanner
Wed Feb 08, 2012 12:50 pm
Forum: Sequence Improvement Questions
Topic: Contig end question
Replies: 2
Views: 5032

Re: Contig end question

Thanks a bunch Wilson!
by bdanner
Wed Feb 01, 2012 9:16 pm
Forum: Sequence Improvement Questions
Topic: Contig end question
Replies: 2
Views: 5032

Contig end question

We are wondering where to call the ends on contig5-1041G20. At the left most end we see a lot of X's which signifies a vector in two of the reads and are wondering if we should call the end there. On the right most end we see X's in the reads as well and are wondering if we have the correct placemen...