Search found 14 matches

by cmackinnon
Wed Apr 03, 2013 2:47 am
Forum: Annotation Questions
Topic: D biarmipes contig 31 exon 14
Replies: 1
Views: 3814

D biarmipes contig 31 exon 14

The gene record finder shows there are 3 isoforms for the zfh2 gene contained in contig 31. Isoform PC has an exon 14, but the blastx report only shows a *, which I assume is because exon 14 is very small and only the stop codon is detected by the blastx? I have tried to look for overlaps at the end...
by cmackinnon
Mon Sep 24, 2012 5:58 pm
Forum: Annotation Questions
Topic: D. biarmides question
Replies: 4
Views: 5934

Re: D. biarmides question

Thanks again. I needed an explanation for making them do both!
by cmackinnon
Thu Sep 20, 2012 1:36 pm
Forum: Annotation Questions
Topic: D. biarmides question
Replies: 4
Views: 5934

Re: D. biarmides question

Thank you! Cosmid31 has one gene [zfh2] with three isoforms. There are about 16 exons total [haven't carefully counted them yet]. Another question, which blastx report should I use? The blastx information obtained by clicking on the exon in the Genome Browser predicts a better ending nucleotide coor...
by cmackinnon
Wed Sep 19, 2012 3:48 pm
Forum: Annotation Questions
Topic: D. biarmides question
Replies: 4
Views: 5934

D. biarmides question

D. biarmides contig 31 is rated a level 4. Briefly, what should I anticipate in terms of annotation challenges for a level 4 project?
by cmackinnon
Thu Sep 13, 2012 2:23 am
Forum: Annotation Questions
Topic: D. erecta 2nd 3L extended fosmid 32 changes
Replies: 2
Views: 4710

Re: D. erecta 2nd 3L extended fosmid 32 changes

Thank you! I've been having trouble with blastx results--we keep getting error messages---and turning off the low complexity filter seemed to "fix" the problem, but created another one! I'll try a different browser than internet explorer; I tend to have more problems with it when accessing databases.
by cmackinnon
Wed Sep 12, 2012 10:09 pm
Forum: Annotation Questions
Topic: D. erecta 2nd 3L extended fosmid 32 changes
Replies: 2
Views: 4710

D. erecta 2nd 3L extended fosmid 32 changes

In June 2012, my students annotated fosmid 32 of D. erecta, 2nd 3L extended assembly. They selected the sls gene, isoform PD The Gene Record finder at that time showed the sls gene isoform RD started with exon 42. The gene model checker passed with flying colors. Today in class I had the students fi...
by cmackinnon
Mon Apr 02, 2012 2:26 pm
Forum: Annotation Questions
Topic: siz gene in fosmid 20 question
Replies: 3
Views: 5895

Re: siz gene in fosmid 20 question

Thank you! I forgot about the sequence overlaps in fosmids [duh]--guess this counts as April Fool's after all! :-). Another teachable moment! I found the first exon in siz RB. The annotation for siz RB and RA passes Gene Recorder Finder; haven't finished RC, but will let you know if I have problems!
by cmackinnon
Sun Apr 01, 2012 8:37 pm
Forum: Annotation Questions
Topic: siz gene in fosmid 20 question
Replies: 3
Views: 5895

siz gene in fosmid 20 question

I'm trying to help my students do the siz gene annotation [2008 3L/extended, fosmid 20]. I used the Gene Record Finder's aa sequence for isoform siz-RD exon 1 for the blastx, and the blastx report for exon 1 of siz RD shows a very poor match [Expect = 8.2; identities = 50%. Some of gene models [Twin...
by cmackinnon
Mon Nov 14, 2011 4:32 pm
Forum: Annotation Questions
Topic: Different amino sequence in blastx report and genome browser
Replies: 3
Views: 5716

Re: Different amino sequence in blastx report and genome bro

Thank you for the explanation. Should students routinely check Flybase Blastx, or only if there's a problem like this one?
by cmackinnon
Thu Nov 10, 2011 2:15 pm
Forum: Annotation Questions
Topic: Different amino sequence in blastx report and genome browser
Replies: 3
Views: 5716

Different amino sequence in blastx report and genome browser

My students are working with D. erecta 3L extended fosmid 20. They used Gene Record Finder to get the amino acid for siz-RD, exon 8. When the NCBI blastx is done, the blast report shows that the amino acid match is missing the first dozen or so of the amino acid sequence [HPHVNLLHAAEPHYYNAQALPQGAAYY...
by cmackinnon
Sun Aug 01, 2010 5:45 pm
Forum: Annotation Questions
Topic: Student presentation of D. erecta contig 36 available?
Replies: 2
Views: 3882

Report formats

Hi Wilson. Thanks for the guidance. The student reports have different formats (which is to be expected, but also confusing). I rediscovered Chris Shaffer's 2009 Annotation to D. mojavensis and it seems to be a better starting point. It helped clarify that RepeatMasker, Clustal, and Synteny analyses...
by cmackinnon
Thu Jul 29, 2010 2:26 pm
Forum: Annotation Questions
Topic: Student presentation of D. erecta contig 36 available?
Replies: 2
Views: 3882

Student presentation of D. erecta contig 36 available?

At the 2010 June workshop, a student presented his/her annotation of D. erecta contig 36. Is that powerpoint available to faculty? I'm developing a practice activity and would like to have an "answer key" for teaching purposes.
by cmackinnon
Tue Jul 27, 2010 5:25 pm
Forum: Annotation Questions
Topic: Question 3 in "A Simple Annotation Problem" handou
Replies: 2
Views: 3884

I think I found the answer

Using Ruth Howe's notes, I see I need to check the box to align two or more sequences in the NCBI BLAST blastx choice. The query sequence is fosmid's DNA [obtained from the UCSC Genome Browser] and the subject sequence is the Gene Record Finder polypeptide details of the first exon. Let's see if I c...
by cmackinnon
Tue Jul 27, 2010 4:30 pm
Forum: Annotation Questions
Topic: Question 3 in "A Simple Annotation Problem" handou
Replies: 2
Views: 3884

Question 3 in "A Simple Annotation Problem" handou

I'm confused by the instructions on pg 4, question 3 on mapping each exon using BLAST searches. The instructions state: "Go to the NCBI BLAST search site and compare the protein sequence of the first coding exon of PMCA to the entire fosmid sequence." The last sentence states: Using blastx the resul...