Search found 211 matches

by cshaffer
Wed Nov 18, 2009 1:55 am
Forum: Annotation Questions
Topic: Regions of high homology with no genes
Replies: 1
Views: 5972

conservation without gene predictions

yes that region to the left is quite curious. Gene predictors do have a false negative rate and sometimes miss a gene completely. It is also possible that there is only a partial gene here (the rest would be off the end of the clone) in which case the gene predictors might be fooled into thinking th...
by cshaffer
Fri Oct 30, 2009 12:29 pm
Forum: Frequently Asked Questions
Topic: IRB at GEP member institutions
Replies: 0
Views: 15103

IRB at GEP member institutions

A note from Sally which may answer your questions about obtaining IRB's at your institution: Check with the chairman of your IRB. We have found that some schools are happy to give approval based on the review by Washington University, given copies of the approval forms, given that Wash U judged that...
by cshaffer
Wed May 06, 2009 2:28 pm
Forum: Funding Opportunities
Topic: cofactor genomics award of a Illumina run
Replies: 6
Views: 31636

message from Eric Spana

Hi Sally-

I checked with David MacAlpine, and he's submitting a grant to sequence a bunch of Dmel cell lines, so that doesn't seem like an avenue worth pursuing for that company's grant.

Eric
by cshaffer
Wed May 06, 2009 12:05 pm
Forum: Funding Opportunities
Topic: cofactor genomics award of a Illumina run
Replies: 6
Views: 31636

posting message from Eric Spana

Hi Sally- My first thought is a Dmel cell line like S2, or Kc or some other--it may be underway from the modencode project though. A professor here at Duke (David MacAlpine) has some CGH data for cell lines that is pretty interesting. I can check with him to see if there is any sequencing on the hor...
by cshaffer
Wed May 06, 2009 12:03 pm
Forum: Funding Opportunities
Topic: cofactor genomics award of a Illumina run
Replies: 6
Views: 31636

posting message from Yuying Gosser

Dear Dr. Elgin,

We would like to participate in this project. If you write
the proposal, please include the CCNY team.
Thank you.

Yuying
by cshaffer
Mon May 04, 2009 1:37 pm
Forum: Funding Opportunities
Topic: cofactor genomics award of a Illumina run
Replies: 6
Views: 31636

cofactor genomics award of a Illumina run

Dear colleagues, Cofactor Genomics is planning to donate a Illumina run to the undergraduate class/group who comes up with the best project - ~700Mb of new DNA sequence! Applications are due by the end of May. You can read all about if at http://www.cofactorgenomics.com/classroom.php . Should we put...
by cshaffer
Thu Apr 09, 2009 11:45 pm
Forum: Annotation Questions
Topic: Large chromosomal duplications, and repeated hits for same g
Replies: 3
Views: 9358

following up on BLAST hits

I would say it depends on how different the best hit alignment and 2nd hit alignment are. if both alignments are very close in quality it may be that you have a gene family of closely related proteins and it can be difficult to pick the right member of the family. The good news here is that genes ra...
by cshaffer
Thu Apr 09, 2009 11:29 pm
Forum: Annotation Questions
Topic: BLAST hit to single exon coding gene with no methionine?
Replies: 5
Views: 11529

finding the large orf

I noticed the ORF simply using the browser and noticing there were no stop codons. This is a slow and manual process. To see it make sure that the "Base position" track is on full. As you zoom in you will soon see three bars on the track which are the translation of three frames. for example try thi...
by cshaffer
Fri Apr 03, 2009 6:03 pm
Forum: Sequence Improvement Questions
Topic: Vector sequence
Replies: 2
Views: 8434

vector sequence and finding the ends

We know that the correct vector sequence was put in the edit dir for each project. But it could be that your set up on your computers is using a different vector file. Be sure when the student enter the complere path to the vector sequence in the edit_dir with their project and they pick the "pcc01....
by cshaffer
Sun Mar 29, 2009 1:07 am
Forum: Annotation Questions
Topic: BLAST hit to single exon coding gene with no methionine?
Replies: 5
Views: 11529

more investigations into 52.2

More updates: If you look at the region around 52.2 you will find that there is a single huge open reading frame on the opposite strand that extends from 37500 to 34000. That is an open reading frame of about 2500 bases! What are the chances that would happen in a random sequence? Some of the region...
by cshaffer
Sun Mar 29, 2009 12:01 am
Forum: Annotation Questions
Topic: BLAST hit to single exon coding gene with no methionine?
Replies: 5
Views: 11529

CG41280

Ok I have looked into CG41280. It was published as part of the heterochromatin project. I also looked at CG41281 which is the next gene down from CG41280. Neither protein has a Met at the start nor a stop codon. I am guessing that many of these heterochromatin genes are simply partial genes or singl...
by cshaffer
Sat Mar 28, 2009 8:22 pm
Forum: Annotation Questions
Topic: BLAST hit to single exon coding gene with no methionine?
Replies: 5
Views: 11529

differences between Flybase and ENSEMBL

Flybase has gone to a system of updating the drosophila genome annotation set about once every 6 weeks. This is great news for biologists working on flies that want the most up-to-date info on the genome but bad news for us and anyone else who is trying to maintain some kind of subset of the data. E...
by cshaffer
Sun Mar 22, 2009 4:58 am
Forum: Annotation Questions
Topic: bl2seq output format questions
Replies: 1
Views: 6073

masking

I have seen XXXX and grey letters but never both in the same alignment. I think this is new with the recent new version of BLAST that NCBI put out. Both of these are are examples of masking low complexity sequence. In this version of BLAST they call them "filtering" and "masking". These two types of...
by cshaffer
Thu Mar 19, 2009 3:09 am
Forum: Alumni Workshop
Topic: June 2009 Alumni workshop
Replies: 1
Views: 10102

June 2009 Alumni workshop

GEP members, The first alumni workshop of the summer of 2009 will be May 31st - June 2. We need to start thinking about the next science education article and the upcoming HHMI competitive renewal. This topic has been created to discuss these issues and others that may come up regarding the workshop.
by cshaffer
Wed Mar 18, 2009 7:46 pm
Forum: Sequence Improvement Questions
Topic: new finishing tactic
Replies: 1
Views: 6295

duplicated fosmid

Yeah Sorry if we did not make this clear. To make everything work over at the Genome center each clone needs a unique name. As you may recall we had decided to do each fosmid at least twice, both at the Genome Center and with the GEP crowd. So to be compatible with the genome center we took each fos...