Search found 185 matches

by wleung
Thu Feb 07, 2013 3:40 am
Forum: Sequence Improvement Questions
Topic: good digest, (some) bad read pairs
Replies: 3
Views: 18522

Re: good digest, (some) bad read pairs

If all four restriction digests matched and there are no issues with the assembly in this region (e.g. high quality discrepancies, unaligned high quality, etc), then I would not be too concerned about the inconsistent mate pairs. In particular, if the inconsistent mate pairs are in the correct relat...
by wleung
Thu Feb 07, 2013 2:08 am
Forum: Sequence Improvement Questions
Topic: Polymorphism frequency in ananassae?
Replies: 1
Views: 8394

Re: Polymorphism frequency in ananassae?

Many of the genuine high quality discrepancies I have seen in the D. ananassae projects are placed in regions that matched known transposons in D. ananassae . The consensus sequences in the repetitive regions are marked with blue "repeat" tags. Consequently, some of the high quality discrepancies co...
by wleung
Thu Feb 07, 2013 1:47 am
Forum: Sequence Improvement Questions
Topic: What is calc_total_fragSizes.pl doing?
Replies: 1
Views: 8435

Re: What is calc_total_fragSizes.pl doing?

The calc_total_fragSizes.pl script parses the file which contains the observed fragment sizes in the real digests (i.e. fragSizes.txt ) and calculates the sum of the fragment sizes for each of the real digests. We expect the real digest sizes to be approximately the same for all four restriction dig...
by wleung
Thu Jan 10, 2013 11:00 pm
Forum: Annotation Questions
Topic: How do you know that....
Replies: 1
Views: 7503

Re: How do you know that....

You are correct that the GEP annotation strategy would not allow you to annotate species-specific gene (e.g. genes that are only found in D. biarmipes). The problem is that we cannot confidently construct the gene models using only RNA-seq data. For example, while the oases and cufflinks transcripts...
by wleung
Mon Jan 07, 2013 4:40 am
Forum: GEP Web System Updates
Topic: Changes to the GEP Web Framework - Spring 2013
Replies: 0
Views: 10279

Changes to the GEP Web Framework - Spring 2013

The GEP web framework has been reset for the Spring 2013 semester. Summary of key changes 1. New D. ananassae annotation projects from the 3L reference region available 2. Updated GEP Web Framework and annotation materials (Note: new NCBI BLAST output format) 3. D. ananassae sequence improvement pro...
by wleung
Fri Nov 09, 2012 4:12 pm
Forum: Annotation Questions
Topic: Mutation or sequencing error?
Replies: 1
Views: 8009

Re: Mutation or sequencing error?

The change in the genomic sequence is unlikely to be an error in the consensus because there multiple RNA-seq reads aligned to this region and they agree with the consensus. A FlyBase TBLASTN search of the first CDS of the C isoform (17_1548_0) against the genomic assemblies in different Drosophila ...
by wleung
Thu Nov 01, 2012 4:20 pm
Forum: Annotation Questions
Topic: Gene Model Check Dot Plot Analysis
Replies: 2
Views: 13933

Re: Gene Model Check Dot Plot Analysis

In general, we expect to find some short spurious matches in the dot plot. Some of these matches can occur by chance and others can be attributed to repetitive or low complexity sequences. In fact, this is one of the reasons why we use the BLAST E-value threshold and the low complexity filter to try...
by wleung
Thu Nov 01, 2012 4:05 pm
Forum: Annotation Questions
Topic: Finding Elusive Exons in D. biarmipes
Replies: 3
Views: 12728

Re: Finding Elusive Exons in D. biarmipes

Missing exons in CG33978 Given that exons 3_1556_1 and 2_1566_1 overlap with each other in D. melanogaster , I would try to map the larger exon (3_1556_1) first. From your previous analysis of the adjacent exons, we know that we need this exon to have a phase 1 acceptor and a phase 0 donor and that...
by wleung
Thu Nov 01, 2012 3:43 pm
Forum: Annotation Questions
Topic: Finding Elusive Exons in D. biarmipes
Replies: 3
Views: 12728

Re: Finding Elusive Exons in D. biarmipes

In both cases, the exons are likely to be too small or too weakly conserved to be detected using BLAST searches. Given the lack of expression data, conservation and computational predictions, we will use conservation of exon length and biological constraints to help us pick the best candidate. Missi...
by wleung
Mon Oct 15, 2012 2:41 pm
Forum: Annotation Questions
Topic: Gene model checker, in frame stop codons
Replies: 1
Views: 11257

Re: Gene model checker, in frame stop codons

Yes, in frame stop codons in the gene model is typically caused by incompatible splice donor and acceptor sites. When the sum of the donor and acceptor phases is not either 0 or 3, it will introduce a frame shift in the translation. In most cases, translating in the incorrect reading frame would res...
by wleung
Thu Sep 20, 2012 2:32 pm
Forum: Annotation Questions
Topic: D. biarmides question
Replies: 4
Views: 12816

Re: D. biarmipes question

> Will I miss important info if I only use the blastx from the genome browser or should I still do a NCBI blastx as a double check of the coordinates? Yes, because the blastx alignment track on the genome browser is created by searching the contig sequence against the set of full-length D. melanogas...
by wleung
Wed Sep 19, 2012 8:02 pm
Forum: Annotation Questions
Topic: D. biarmides question
Replies: 4
Views: 12816

Re: D. biarmides question

Because D. biarmipes is evolutionarily further away from D. melanogaster than D. erecta , we anticipate that the D. biarmipes projects will be more difficult to annotate than D. erecta . The difficulty levels of the D. biarmipes projects range from 4 to 6, with 4 being the easiest. D. biarmipes proj...
by wleung
Thu Sep 13, 2012 1:50 am
Forum: Annotation Questions
Topic: D. erecta 2nd 3L extended fosmid 32 changes
Replies: 2
Views: 10373

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

As you have mentioned, the gene record for the D. melanogaster sls gene has changed in June 2012. flybase_sls_update.png However, the most likely reason that you cannot detect the first exon (43_374_0) with blastx is that the low complexity filter and compositional adjustments were on when you perfo...
by wleung
Thu Aug 30, 2012 8:15 pm
Forum: Annotation Questions
Topic: last codon codes just for a stop codon
Replies: 1
Views: 7795

Re: last codon codes just for a stop codon

> Do I need to recheck the gene model? No, you can ignore the warning from the Gene Model Checker in this case. Having a stop codon at the beginning of the last coding exon is unusual and it merits additional explanations in the GEP Annotation Report. However, the explanation in the Annotation Repor...
by wleung
Sat Aug 25, 2012 5:52 pm
Forum: GEP Web System Updates
Topic: Changes to the GEP Web Framework - Fall 2012
Replies: 0
Views: 11352

Changes to the GEP Web Framework - Fall 2012

Hello Everyone, The Project Management System has been reset for Fall 2012. A new set of 70 projects derived from the Muller F element of D. biarmipes is now available to be claimed on the Project Management System. You can view the projects using the GEP UCSC Genome Browser Mirror by selecting “D. ...