Search found 10 matches

by nkokan
Thu Apr 10, 2014 6:07 am
Forum: Annotation Questions
Topic: Frame disagreement between browser and Blastx alignments
Replies: 4
Views: 7115

Re: Frame disagreement between browser and Blastx alignments

I repeated the blastx with compositional matrix "no adjustment" and filters turned off and I got an alignment in -2 frame with the same predicted coordinates that you posted earlier. I think the issue with -3 frame that the student had might have been due to the parameters being not set correctly. I...
by nkokan
Thu Apr 10, 2014 2:37 am
Forum: Annotation Questions
Topic: Frame disagreement between browser and Blastx alignments
Replies: 4
Views: 7115

Re: Frame disagreement between browser and Blastx alignments

That is great to see a -2 frame but I still have to resolve the -3 frame issue as she ran these twice. We used DNA from the Gander Browser "get DNA" feature for the contig. My student was unable to open the sequence file in the src folder. I will re run the blastx with the project sequence file and ...
by nkokan
Wed Apr 09, 2014 10:57 pm
Forum: Annotation Questions
Topic: Frame disagreement between browser and Blastx alignments
Replies: 4
Views: 7115

Frame disagreement between browser and Blastx alignments

We are working with Dbiarmipes dot_Aug2013_contig1, feature 1.1 (PlexB ortholog). Blastx alignments gave the following predicted coordinates, 13042-12542 in frame -3 for the exon. In the browser, we found stop codons for the exon in this region in frame -3. However, there is a start codon at 13042 b...
by nkokan
Wed Apr 06, 2011 2:13 am
Forum: Annotation Questions
Topic: Adding Custom Tracks
Replies: 1
Views: 3607

Adding Custom Tracks

How can I add custom tracks in the Genome Browser for annotations? I see the custom tracks of the gene from the Gene Model Checker but not in the mirror browser site. I do not understand the file formats for the upload. Are there instructions for this somewhere?
nkokan
by nkokan
Wed Mar 23, 2011 4:45 pm
Forum: Annotation Questions
Topic: D. grimshawi contig18
Replies: 1
Views: 3366

D. grimshawi contig18

We just started working on our annotation research projects. By examining the contig in the UCSC genome browser mirror site, we see that there are no blastx alignments to any Dmel proteins for this contig. However, the Genscan gene predictions and several other gene prediction models have predicted ...
by nkokan
Fri Apr 30, 2010 11:58 am
Forum: Alumni Workshop
Topic: Prokaryotic Annotation Grant
Replies: 3
Views: 8050

Prokaryotic Annotation

Anne,
I too am interested in prokaryotic annotation for a microbiology Lab class and a bioinormatics course taught in fall. I will interested in hearing more about the project.

Nighat
by nkokan
Thu Apr 15, 2010 5:32 pm
Forum: Annotation Questions
Topic: Gene Record Finder Polypeptide Details
Replies: 1
Views: 3316

Gene Record Finder Polypeptide Details

In Ensembl, the amino acids forming the the exon intron bounderies are color coded as red, this is not the case in the polypeptide details of the Gene Record Finder. Are there any advantages or disadvantages for indicating these amino acids to be in split codons when students annotate their contigs?
by nkokan
Wed Apr 29, 2009 7:08 pm
Forum: Annotation Questions
Topic: Annotation of D erecta
Replies: 3
Views: 5301

Orthologous Genes

Thanks for your input Chris. I have another question... Can one gene be on the forward strand in one species and be on the reverse strand in another species? I don't know if I am saying it right. I am finding that the two orthologs for the putative genes in D erecta we are annotating are on the plus...
by nkokan
Mon Apr 27, 2009 4:16 am
Forum: Annotation Questions
Topic: Gene Record Finder
Replies: 1
Views: 3659

Gene Record Finder

What is "Unique" in the Gene Record Finder?
How and when can it be used during the annotation?
Thanks,
Nighat Kokan
by nkokan
Sat Apr 25, 2009 9:22 pm
Forum: Annotation Questions
Topic: Annotation of D erecta
Replies: 3
Views: 5301

Annotation of D erecta

I did a tblastn search on a one exon gene from Dmel against contig 14 in D erecta. I got 4 hits, 3 of them are in the + frames, two in +1 and one in +3 with 97-100% identities but the fourth one is in the minus frame (-1). This last alignment gave only 39% identity. How do I interpret the minus fram...