Search found 211 matches

by cshaffer
Wed Feb 11, 2009 10:00 pm
Forum: Sequence Improvement Questions
Topic: Submitting finishing reactions
Replies: 2
Views: 7080

problems with uploading

ken,
I have forwarded your request to wilson. To help wilson can you post the OS version and yes it probably matters which version of IE and firefox. You can get the version number from the "help" menu "about" item in both browsers.
by cshaffer
Wed Feb 11, 2009 5:37 pm
Forum: Sequence Improvement Questions
Topic: finishing will start soon
Replies: 2
Views: 7841

end of sequencing

Laura,
I am sure we can work something out. I will talk to Sally about this and get back to you.
chris
by cshaffer
Thu Feb 05, 2009 10:11 pm
Forum: Annotation Questions
Topic: frame inconsistencies between databases
Replies: 1
Views: 5960

which frame

I have seen different programs number the various frames differently it sounds like the goose server and bl2seq may be numbering them differently. The good news is that as long as you have the whole gene in the fosmid the frame will be irrelevant in the long run. What you really need to know is the ...
by cshaffer
Thu Feb 05, 2009 9:59 pm
Forum: Sequence Improvement Questions
Topic: finishing in grimshawi: plasmids or BACs?
Replies: 2
Views: 7896

they are all fosmids

yes all we have here are the fosmid clones All the small 2-4 kb inserts were thrown out and not submitted to the clone bank. We were lucky in that about 20% of the fosmids were kept and submitted so that we could get them sent to us. So always pick primers using the Clone option. if you are in a rep...
by cshaffer
Wed Feb 04, 2009 2:39 am
Forum: Sequence Improvement Questions
Topic: Another finishingHomework question-picking primers
Replies: 3
Views: 8875

what is "editable"

Reasonable people can certainly disagree on what can simply be "edited" and where you need new data. I have even heard professional finishers disagree on this. This is data interpretation and everyone should feel empowered to stick to their own feelings in these matters. Feel free to err on the side...
by cshaffer
Wed Feb 04, 2009 2:34 am
Forum: Sequence Improvement Questions
Topic: Another finishingHomework question-picking primers
Replies: 3
Views: 8875

what to do when nothing meets all criteria

Wilson made up the answer sheet and I think he is correct in that you can just edit, but I did not require this answer from my students. This is because this situation is not that uncommon. It does come up from time to time when working with real data and sometimes you will have to pick a primer fro...
by cshaffer
Fri Jan 23, 2009 6:39 pm
Forum: Frequently Asked Questions
Topic: finishing read schedule
Replies: 0
Views: 11386

finishing read schedule

Q: What is the current schedule for ordering finishing reads and getting results back? A: In 2009 the system will run from January 28th and run for 8-10 weeks (the exact end is yet to be determined). Those of us here at the GEP will do our best to keep to this schedule: 1 orders must be submitted by...
by cshaffer
Fri Jan 23, 2009 6:34 pm
Forum: Sequence Improvement Questions
Topic: finishing will start soon
Replies: 2
Views: 7841

finishing will start soon

Just a reminder in case you missed it: Dear colleagues, The system is now active for claiming projects and ordering reads. We will collect the first set of orders for sequencing at midnight Wednesday, January 28. Our current plan is to continue for 8 to 10 weeks, depending on demand (last order bein...
by cshaffer
Mon Nov 10, 2008 8:05 pm
Forum: Sequence Improvement Questions
Topic: phrap skipping reads
Replies: 1
Views: 5986

problems with "add new reads"

It is hard to diagnose without more information. There are a bunch of ways that add new reads tends to fail. First make sure the reads are in the chromat_dir also the names of the files must be UNIX compliant not mac compliant. So no spaces in the names of the files. also the *.fof file that you use...
by cshaffer
Fri Aug 29, 2008 6:11 pm
Forum: Sequence Improvement Questions
Topic: crossmatch error
Replies: 18
Views: 35539

cross_match

I don't know why you are missing cross_match it is part of the package that you download. Maybe it got deleted or corrupted. Anyway I will send you a copy of cross_match by email. You will have to copy it to the /usr/local/genome/bin directory on your 10.3 machine. This may work, but you may also ne...
by cshaffer
Tue Apr 29, 2008 10:23 pm
Forum: Annotation Questions
Topic: missing 5' exons without homology
Replies: 1
Views: 5896

missing initial exon

These kinds of situations are indeed difficult. While erecta and melanogaster are indeed very similar it can be hard to find some exons. I have a few questions you should also consider if you have not done so: is it possible that the missing exon is off the end of your fosmid? when using BLAST did y...
by cshaffer
Fri Apr 25, 2008 8:52 pm
Forum: Annotation Questions
Topic: alternative 5' UTR
Replies: 5
Views: 13610

UTR's in Erecta

Some groups have been successful in finding probable UTR's by sequence similarity with melanogaster annotated UTR's but we are not asking everyone to do this. Just the coding is O.K.
by cshaffer
Fri Apr 25, 2008 4:04 pm
Forum: Annotation Questions
Topic: gene off end of fosmid
Replies: 1
Views: 6093

gene checker for partial genes

There is a pull down menu (translation) that you need to set to tell the checker you have a partial gene. In your case set the value to "missing 5' end of translated region". You also need to tell the gene checker if you have a partial codon at the beginning of the first exon you have in your fosmid...
by cshaffer
Fri Apr 25, 2008 3:55 pm
Forum: Annotation Questions
Topic: alternative 5' UTR
Replies: 5
Views: 13610

UTR mapping in mojavensis

D mojavensis and D melanogaster are too distant to detect UTR's by any similarity based search. The only way to find UTR's would be to match CDNA clone sequences back to the genome. There are no cDNA sequences for mojavensis and only a handful of EST's so we are not asking schools to map UTR's in mo...
by cshaffer
Tue Apr 22, 2008 8:02 pm
Forum: Annotation Questions
Topic: Frames and Finding Start and Stop Codons
Replies: 1
Views: 8598

frames and start and stop codons

First just to be clear, only the first exon in any gene model needs to start with a ATG start codon, likewise only the last exon will end with a stop codon. With respect to these exons the start and stop codons must be in the same frame as the other amino acids that are similiar to the d melanogaste...