Search found 11 matches

by mshaw
Wed Mar 25, 2015 3:36 pm
Forum: Annotation Questions
Topic: Not all of the gene in the contig?
Replies: 1
Views: 1129

Not all of the gene in the contig?

I have a student who is working on annotating Caps in D. elgans. Exons 3, 4, 5 6 are present with very high sequence homology but even with less stringent parameters homology with any of the other exons is very low. RNAseq data indicates expression of exons 3-6. It is a huge gene in Dm with an intro...
by mshaw
Fri Jun 20, 2008 2:43 pm
Forum: Maize Genome Annotation Project
Topic: Maize genome project
Replies: 1
Views: 4543

Maize genome project

I am interested in this project. How could my student's or I contribute? :?:
Mary Shaw
by mshaw
Mon Apr 30, 2007 2:57 pm
Forum: Annotation Questions
Topic: End of Gene
Replies: 1
Views: 367

End of Gene

Do we report the stop codon as the end of the gene or the last condon that codes for an amino acid?
by mshaw
Tue Apr 24, 2007 3:50 pm
Forum: Sequence Improvement Questions
Topic: ace.0 file
Replies: 1
Views: 293

ace.0 file

How do we create the ace.o file and the gtar-gzip files?
by mshaw
Tue Apr 03, 2007 12:11 am
Forum: Annotation Questions
Topic: scaffold number
Replies: 2
Views: 470

scaffolds

It works for us now too!
by mshaw
Fri Mar 30, 2007 8:53 pm
Forum: Annotation Questions
Topic: scaffold number
Replies: 2
Views: 470

scaffold number

When we enter the scaffold number given for our sequences, 4512, at the UCSC browser it says that it can't find that scaffold and takes us to 4929 which is says is the closest one. Any suggestions?
by mshaw
Fri Mar 30, 2007 8:49 pm
Forum: Sequence Improvement Questions
Topic: More sequncing checklist questions
Replies: 1
Views: 339

More sequncing checklist questions

There are several items that we don't understand/know how to do.
1). What are "PCR only regions" and how do we find them?
2) What does "assembly pieces used" mean?
3) how do we "run findit"?
by mshaw
Fri Mar 30, 2007 8:35 pm
Forum: Sequence Improvement Questions
Topic: checklist issue: BLAST check
Replies: 3
Views: 434

Blast

I presume that this is a Blastn search. How do we get the sequence out of consed to use?
by mshaw
Tue Mar 27, 2007 4:53 pm
Forum: Sequence Improvement Questions
Topic: vector end sequences (?)
Replies: 2
Views: 364

vector sequences

This didn't find anything for us. How about for others?
Mary Shaw
by mshaw
Tue Mar 27, 2007 4:08 pm
Forum: Sequence Improvement Questions
Topic: Restriction digests
Replies: 1
Views: 394

Restriction digests

After adding what we think is the file name for the vector sequences we get the message "No such files exists". We think that the file name should be users/bio4342/desktop/mshaw_070209141429/355-J17/edit_dir/pCC01.fasta. We double checked the address, tried moving the file to the desktop (out of the...
by mshaw
Wed Mar 14, 2007 11:32 pm
Forum: Annotation Questions
Topic: Drosophila erecta annotation
Replies: 1
Views: 425

Drosophila erecta annotation

Has anyone else worked on the Drosophila erecta annotation? We are just getting started and I would be interested in any advice.
Mary Shaw