Search found 185 matches
- Thu May 02, 2013 7:59 pm
- Forum: Annotation Questions
- Topic: Submitting Annotation report for a gene desert fosmid
- Replies: 1
- Views: 7298
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...
- Thu May 02, 2013 3:49 pm
- Forum: Annotation Questions
- Topic: aanotation query for gene missing both 3' and 5' end
- Replies: 1
- Views: 9158
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.
- Wed Apr 24, 2013 10:34 pm
- Forum: Annotation Questions
- Topic: How to report a new gene
- Replies: 1
- Views: 7450
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...
- Tue Apr 23, 2013 2:02 am
- Forum: Annotation Questions
- Topic: BLASTp search for final submission item
- Replies: 1
- Views: 8886
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...
- Tue Apr 23, 2013 1:49 am
- Forum: Annotation Questions
- Topic: scaffold map for biarmipies annotation?
- Replies: 1
- Views: 7468
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...
- Thu Apr 18, 2013 10:10 pm
- Forum: Annotation Questions
- Topic: Gene aligned using BlastX not present on desired chromosome?
- Replies: 1
- Views: 7333
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...
- Thu Apr 18, 2013 1:14 am
- Forum: Annotation Questions
- Topic: how to report a microRNA?
- Replies: 1
- Views: 7839
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.
- Thu Apr 18, 2013 1:11 am
- Forum: Annotation Questions
- Topic: gene missing from Gene Record Finder
- Replies: 2
- Views: 10017
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:
- Thu Apr 11, 2013 8:05 pm
- Forum: Annotation Questions
- Topic: Query regarding PROJECT SUBMISSION..
- Replies: 1
- Views: 8000
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...
- Tue Apr 09, 2013 2:34 am
- Forum: Annotation Questions
- Topic: dot plot adjustability?
- Replies: 1
- Views: 8147
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...
- Thu Apr 04, 2013 7:14 pm
- Forum: Annotation Questions
- Topic: query regarding annotation submission report
- Replies: 1
- Views: 7769
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...
- Wed Apr 03, 2013 5:45 am
- Forum: Annotation Questions
- Topic: D biarmipes contig 31 exon 14
- Replies: 1
- Views: 8218
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...
- Tue Mar 26, 2013 5:20 am
- Forum: Annotation Questions
- Topic: Spurious blastX result
- Replies: 1
- Views: 8344
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...
- Thu Mar 21, 2013 10:42 pm
- Forum: Annotation Questions
- Topic: Same gene present on two different fosmids
- Replies: 1
- Views: 7836
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...
- Fri Mar 08, 2013 2:03 am
- Forum: Sequence Improvement Questions
- Topic: Infamous Red Tirangles
- Replies: 1
- Views: 9685
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...