Search found 185 matches

by wleung
Thu May 02, 2013 7:59 pm
Forum: Annotation Questions
Topic: Submitting Annotation report for a gene desert fosmid
Replies: 1
Views: 3819

Re: Submitting Annotation report for a gene desert fosmid

To submit a project without any genes, you can create a plain text file (e.g. using TextEdit on the Mac, WordPad on Windows) with the message "No genes found in project" and save the file with the .gff extension. You can then create two additional copies of this file and change the file extension to...
by wleung
Thu May 02, 2013 3:49 pm
Forum: Annotation Questions
Topic: aanotation query for gene missing both 3' and 5' end
Replies: 1
Views: 3995

Re: annotation query for gene missing both 3' and 5' end

If the isoforms in D. melanogaster use different unique sets of coding exons, please list each isoform as unique in the Annotation Report irrespective of whether the exons that are present in your project are shared across all the isoforms.
by wleung
Wed Apr 24, 2013 10:34 pm
Forum: Annotation Questions
Topic: How to report a new gene
Replies: 1
Views: 3890

Re: How to report a new gene

If your analysis indicates that there might be a novel paralog in D. ananassae , you can pick an unique name for the feature (i.e. a gene symbol that has not been used in D. melanogaster ). For example, a novel paralog of CG32395 could be called CG32395-2. When you check the gene model using the Gen...
by wleung
Tue Apr 23, 2013 2:02 am
Forum: Annotation Questions
Topic: BLASTp search for final submission item
Replies: 1
Views: 3948

Re: BLASTp search for final submission item

The primary purpose of the blastp search of the Genscan predictions against the nr database is to identify genes that are found in other species but not in D. melanogaster . Consequently, the blastp search should be against all of the non-redundant protein database (i.e. not limited to D. melanogast...
by wleung
Tue Apr 23, 2013 1:49 am
Forum: Annotation Questions
Topic: scaffold map for biarmipies annotation?
Replies: 1
Views: 3902

Re: scaffold map for biarmipies annotation?

The D. biarmipes projects are in order so contig48 and contig50 overlaps with contig49. I have created a new D. biarmipes project page on the GEP public wiki. The page contains a link to a text file with the exact location of each annotation project relative to the whole genome assembly. You can sea...
by wleung
Thu Apr 18, 2013 10:10 pm
Forum: Annotation Questions
Topic: Gene aligned using BlastX not present on desired chromosome?
Replies: 1
Views: 3779

Re: Gene aligned using BlastX not present on desired chromos

Previous analysis by Bhutkar et al. shows that ~95% of the D. melanogaster genes stay on the same Muller element across the 12 Drosophila species. This means that while gene movement across different Muller elements are rare, they do occur ~5% of the time. When trying to identify the putative orthol...
by wleung
Thu Apr 18, 2013 1:14 am
Forum: Annotation Questions
Topic: how to report a microRNA?
Replies: 1
Views: 3819

Re: how to report a microRNA?

Please include the annotation of the microRNA in GEP Annotation report form. Because our current analysis is only focused on protein-coding genes, no additional files would need to be submitted in conjunction with this annotation.
by wleung
Thu Apr 18, 2013 1:11 am
Forum: Annotation Questions
Topic: gene missing from Gene Record Finder
Replies: 2
Views: 4929

Re: gene missing from Gene Record Finder

The Gene Record Finder uses the FlyBase gene symbol as the unique identifier for D. melanogaster genes. In this case, the official gene symbol for taiman is tai. The gene record is available on the Gene Record Finder:
gene_record_tai.png
gene_record_tai.png (165.71 KiB) Viewed 4928 times
by wleung
Thu Apr 11, 2013 8:05 pm
Forum: Annotation Questions
Topic: Query regarding PROJECT SUBMISSION..
Replies: 1
Views: 4378

Re: Query regarding PROJECT SUBMISSION..

One of the main reasons to perform the blastx search is to identify genes that might be found in other species but not in D. melanogaster . Consequently, you should include the results of the blastx search against all the species. However, you do not need to include a screenshot of the blastx result...
by wleung
Tue Apr 09, 2013 2:34 am
Forum: Annotation Questions
Topic: dot plot adjustability?
Replies: 1
Views: 4018

Re: dot plot adjustability?

No, the Gene Model Checker does not have the option to align the submitted model against just a part of the D. melanogaster ortholog. However, you can use the NCBI blastp program (with bl2seq) to compare parts of the protein. In addition to the protein alignment, the output from bl2seq include a dot...
by wleung
Thu Apr 04, 2013 7:14 pm
Forum: Annotation Questions
Topic: query regarding annotation submission report
Replies: 1
Views: 3849

Re: query regarding annotation submission report

As part of the initial analysis of the 12 Drosophila genomes, the Drosophila 12 Genomes Consortium generated a set of gene predictions (GLEAN-R) for all the Drosophila species. These predictions are in the NCBI RefSeq database with the prefix XM_ (mRNA) or XP_ (protein). The XM and XP prefixes indic...
by wleung
Wed Apr 03, 2013 5:45 am
Forum: Annotation Questions
Topic: D biarmipes contig 31 exon 14
Replies: 1
Views: 3804

Re: D biarmipes contig 31 exon 14

The basic strategy is to use the placement of the adjacent exons to narrow the scope of the region where the small exon could be placed and then examine the other sources of evidence (e.g. RNA-seq, sequence similarity to untranslated regions) to identify the small exon. In this case, the CDS 14_1629...
by wleung
Tue Mar 26, 2013 5:20 am
Forum: Annotation Questions
Topic: Spurious blastX result
Replies: 1
Views: 4014

Re: Spurious blastX result

The blastx track on the GEP UCSC Genome Browser shows the blastx alignment of full-length D. melanogaster proteins against the D. biarmipes contig. Some of the blastx alignment blocks might be spurious, particularly when the contig only contain part of the protein. In this case, contig49 contains on...
by wleung
Thu Mar 21, 2013 10:42 pm
Forum: Annotation Questions
Topic: Same gene present on two different fosmids
Replies: 1
Views: 3842

Re: Same gene present on two different fosmids

Because the fosmid insert corresponds to a random portion of the D. ananassae genome, the fosmid might end in the middle of a gene. Because the gene olf413 is very highly conserved in D. ananassae , we can map all the CDS's against the D. ananassae 3L assembly using BLAT on the GEP UCSC Genome Brows...
by wleung
Fri Mar 08, 2013 2:03 am
Forum: Sequence Improvement Questions
Topic: Infamous Red Tirangles
Replies: 1
Views: 4306

Re: Infamous Red Tirangles

When you click on the inconsistent mate pairs in Assembly View, Consed should explain the reason why the mate pairs are inconsistent. If the mate pairs are inconsistent because they are oriented away from each other, then it indicates that there is likely a misassembly in the region. In contrast, if...