Search found 45 matches

by ksaville
Wed Apr 24, 2013 6:58 pm
Forum: Annotation Questions
Topic: How to report a new gene
Replies: 1
Views: 4797

How to report a new gene

We believe we have found a duplictaed copy of a gene in D. anananasse. The fosmid is 3L control fosmid_1479A08 and the gene is CG32395. The D mel protein track identified CG32395 and there was a genscan prediction just upstream of this that didn't have a correponding d mel blast hit. A blastp search...
by ksaville
Thu Feb 28, 2013 12:15 am
Forum: Annotation Questions
Topic: Anananasee annotation -missing , extra exons
Replies: 3
Views: 7388

Re: Anananasee annotation -missing , extra exons

Ok Thanks Wilson I will have them include the evidence. I'm basing this on preliminary reports from students and haven't looked into it in detail myself yet, but it seems that a couple had different numbers of exons, with good protein alignments and only a "warn" message that the exon numbers differ...
by ksaville
Wed Feb 27, 2013 9:52 pm
Forum: Annotation Questions
Topic: Anananasee annotation -missing , extra exons
Replies: 3
Views: 7388

Anananasee annotation -missing , extra exons

Are others finding more than usual cases of extra exons or fewer exons when compariing anananasee and melanogaster genes?

We are working on 5 fosmids and have already found 2 or 3 such cases.

K
by ksaville
Mon Feb 25, 2013 8:48 pm
Forum: Annotation Questions
Topic: Annotation report form - isoform naming
Replies: 1
Views: 4848

Annotation report form - isoform naming

Hello In the annotation report form there is a table asking for name of unique isoform based on coding sequence and another column asking for list of isoform with identical coding sequence. We are working with gene Tsp68C from D. Anananassee. In gene record finder, there are 2 isoforms Tsp68C-RA and...
by ksaville
Tue Feb 12, 2013 6:55 pm
Forum: Annotation Questions
Topic: Which projects to claim?
Replies: 2
Views: 6157

Re: Which projects to claim?

That's what I fiured, but thought I'd double check thanks

Ken
by ksaville
Tue Feb 12, 2013 5:30 pm
Forum: Annotation Questions
Topic: Which projects to claim?
Replies: 2
Views: 6157

Which projects to claim?

We are getting ready to claim some annotation projects. I see that there are ananassee and biarmipes projects. Many have been claimed one or more times. What guidelines should we use for claiming projects - in terms of times claimed and times submitted? i.e. Should we base it on number of times subm...
by ksaville
Fri Apr 17, 2009 5:38 pm
Forum: Annotation Questions
Topic: submitting annotation projects
Replies: 1
Views: 3771

submitting annotation projects

hi we're getting close to subitting some annotation projects. However, I have a couple of questions. 1. Do we need to report repeats? and how do we do this. It doesn't seem that there were any specific instructions for this-or maybe I just missed them 2. also, using the annotation report form that o...
by ksaville
Fri Apr 17, 2009 5:27 pm
Forum: Annotation Questions
Topic: finding first exons
Replies: 2
Views: 5175

Thanks

will try first thing next week.

Ken
by ksaville
Thu Apr 16, 2009 6:28 pm
Forum: Annotation Questions
Topic: finding first exons
Replies: 2
Views: 5175

finding first exons

It seems pretty common that our first exons aren't matching anything in BLAST. For example. We have one case-fosmid 22 of D ere (I'm not sure which gene at the moment) For this gene the De exon 2 matches Dm exon 2. Dm has a short exon1 (about 20 aa) which doesn't match well with anything in this fos...
by ksaville
Thu Apr 16, 2009 4:29 pm
Forum: Annotation Questions
Topic: gene checker
Replies: 1
Views: 3914

by the way that was me who posted the last question

I logged in with the other password

ken
by ksaville
Fri Feb 27, 2009 5:04 pm
Forum: Sequence Improvement Questions
Topic: Tandem Repeats?
Replies: 4
Views: 7379

Thanks Chris, I think we can figure out what the consensus should be. There were are a lot of good reads in the region. Our other concerns that is also mentioned above by drevie is that there are reads that go beyond the end read (DGAA ...) to the right. Shouldn't this be all vector past the beginni...
by ksaville
Thu Feb 26, 2009 6:48 pm
Forum: Sequence Improvement Questions
Topic: Tandem Repeats?
Replies: 4
Views: 7379

Tandem Repeats?

There are three different kinds of reads and looks like a misalignment. The end read DGAA-A44E01a.b1 ends, while other reads in this region go past it by roughly 600 bp. We think there is a tandem repeat here and we have torn the different kinds of reads into their own contig. But when we try to pla...
by ksaville
Wed Feb 25, 2009 7:31 pm
Forum: Sequence Improvement Questions
Topic: restriction maps:degree of acceptable diff (real v in-silico
Replies: 3
Views: 6107

same issue

it looks like we're seeing the same thing, at least in one case. a couple of in silico bands below the real bands (8055 v 7306 and 5613 v 5453) then a bunch of bands at 1000 or below that don't show up.
by ksaville
Tue Feb 10, 2009 7:05 pm
Forum: Sequence Improvement Questions
Topic: Submitting finishing reactions
Replies: 2
Views: 4450

update

The inability to browse to the file seems to be specific to the laptops we're using. They're rather old dells and toshibas. We tried both internet explorer and firefox, but I'm not sure of the versions (or if that matters) When I tried from a desktop in the lab, we were able to browse to the file, a...
by ksaville
Tue Feb 10, 2009 6:08 pm
Forum: Sequence Improvement Questions
Topic: Submitting finishing reactions
Replies: 2
Views: 4450

Submitting finishing reactions

Hi

We're having trouble with the project management system. When trying to request reads, we are unable to browse to the ace file. When we click browse-nothing happens

Thanks

Ken