Search found 99 matches

by cjones
Mon Apr 06, 2015 10:34 pm
Forum: Annotation Questions
Topic: Annotation of UTRs?
Replies: 1
Views: 7420

Annotation of UTRs?

Am I right to presume that annotation of D. elegans and D. biarmipes is again coding-sequence only? If there's time at the end of the semester we'll go on to try to annotate TSSs, which will require some UTR mapping, so I wonder if we should annotate the UTRs as well right now.
by cjones
Tue Mar 17, 2015 12:05 am
Forum: Sequence Improvement Questions
Topic: final comment tag location?
Replies: 1
Views: 6265

final comment tag location?

One of the instructions on the finishing checklist says "Add comment tag at the left end of the contig with your name, professor and school" — should that be at the left end of the entire contig, or the left end of the region analyzed by the student?
by cjones
Thu Feb 19, 2015 1:13 am
Forum: Sequence Improvement Questions
Topic: inserting bases into the consensus?
Replies: 1
Views: 5417

inserting bases into the consensus?

One of my students has run into a problem in which the consensus shows 10 T's and a pad between two A's, but there are actually 12 T's there and Consed has simply misaligned things terribly. She can convert the consensus pad to a T (well, okay, a "t") but for the life of me I can't figure out how to...
by cjones
Tue Apr 23, 2013 1:33 am
Forum: Annotation Questions
Topic: BLASTp search for final submission item
Replies: 1
Views: 4171

BLASTp search for final submission item

In the section "Have you annotated all the genes?" students are instructed to perform a BLASTP search against the non-redundant protein database, presumably just of Dmel proteins, using each "region" of their fosmid identified as a potential coding region by each of the gene prediction programs. Mus...
by cjones
Tue Apr 23, 2013 12:14 am
Forum: Annotation Questions
Topic: scaffold map for biarmipies annotation?
Replies: 1
Views: 4125

scaffold map for biarmipies annotation?

I'm trying to identify the fosmid adjacent to 49 (a student has part of a gene near one end and based on the gene structure in Dmel there should be another three exons on the fosmid, but there's no trace of them via BLAST -- has the sequence degenrated or is the intron much larger in biarmipes?) -- ...
by cjones
Thu Apr 18, 2013 1:28 am
Forum: Annotation Questions
Topic: gene missing from Gene Record Finder
Replies: 2
Views: 5227

Re: gene missing from Gene Record Finder

Dang, I don't get it -- I knew the symbol was tai, and tried it, I swear, but got nothing coming back out. How did you update the database between my initial question and your response? ;)
by cjones
Thu Apr 18, 2013 12:33 am
Forum: Annotation Questions
Topic: how to report a microRNA?
Replies: 1
Views: 4039

how to report a microRNA?

One student has found mir-957 on his fosmid; we can't enter it into the Gene Model Checker, so how should we report this, and what (if any) files need to be submitted with it?
by cjones
Wed Apr 17, 2013 11:56 pm
Forum: Annotation Questions
Topic: gene missing from Gene Record Finder
Replies: 2
Views: 5227

gene missing from Gene Record Finder

A student is finding some weak homology to the melanogaster gene taiman in his fosmid, but the gene isn't in the Record Finder. Any suggestions as to how to find the melanogaster sequence broken up by exon, short of a brute force translation of the DNA? I seem to recall that FlyBase used to have thi...
by cjones
Tue Apr 09, 2013 1:09 am
Forum: Annotation Questions
Topic: dot plot adjustability?
Replies: 1
Views: 4243

dot plot adjustability?

Many of my students annotating ananassae are finding themselves with one or two small exons amid vast introns occupying the rest of the fosmid. If the run Gene Model Checker and look at the dot plot, its impossible to interpret if the gene that their small exon is from is large -- they get an essent...
by cjones
Tue Mar 26, 2013 4:24 am
Forum: Annotation Questions
Topic: Spurious blastX result
Replies: 1
Views: 4241

Spurious blastX result

The blastX track for biarmipes contig 49 claims that there is homology to unc-13 (all 6 isoforms) between positions 550 and 600. However, it doesn't match any of the exon sequences for unc-13 in the Gene Record Finder and running blastX with that sequence against Dmel proteins or tblastn with the pu...
by cjones
Thu Feb 28, 2013 1:08 am
Forum: Sequence Improvement Questions
Topic: phrap ignoring "do not overlap" command
Replies: 1
Views: 4473

phrap ignoring "do not overlap" command

A student has labeled a problematic position with "tell phrap not to overlap discrepant reads at this position" (or whatever the literal command is) and then runs phredPhrap. Phrap has once again overlapped reads at this position -- how can we enforce this command? Tearing is of course an option, bu...
by cjones
Thu Feb 28, 2013 12:50 am
Forum: Sequence Improvement Questions
Topic: What to do with a contig that doesn't fit
Replies: 3
Views: 6503

Re: What to do with a contig that doesn't fit

What about contigs that are less than 2 kb long? One of my students has a single contig plus a single read that differs in multiple positions from the contig, suggesting that it belongs elsewhere in the genome. Technically she can't say "Project is in a single contig" as there is that single outlyin...
by cjones
Tue Feb 26, 2013 3:33 am
Forum: Sequence Improvement Questions
Topic: high-frequency peaks?
Replies: 1
Views: 4876

high-frequency peaks?

Does anyone know what's up with these strange reads? I can't recall seeing this before: the peaks are small and compressed horizontally:
by cjones
Thu Feb 14, 2013 2:02 am
Forum: Sequence Improvement Questions
Topic: "Unaligned high quality" must not mean what I think it means
Replies: 1
Views: 4016

"Unaligned high quality" must not mean what I think it means

Why does consed sometimes identify stretches as "unaligned high quality" but, upon inspection, it's a stretch of mixed upper- and lower-case bases, grey or black background, not at all my idea of "high quality"? I told the student dealing with this to simply pull that read (because there were many o...
by cjones
Tue Feb 12, 2013 2:01 am
Forum: Sequence Improvement Questions
Topic: Flybase BLAST vs. UCSC BLAT
Replies: 2
Views: 6151

Flybase BLAST vs. UCSC BLAT

One student pulled two mate pair reads and searched in both BLAT and BLAST to determine if the corresponding subclone belongs in his project or not. FlyBase BLAST placed both reads in the 3L scaffold we're using (#13337), but the BLAT engine on gander gave only a different fosmid for one read and no...