Search found 185 matches

by wleung
Tue Sep 23, 2014 6:32 pm
Forum: Sequence Improvement Questions
Topic: High number HQDs - only one run matches consensu
Replies: 5
Views: 8235

Re: High number HQDs - only one run matches consensu

As you may know, Baylor uses a custom pipeline to create the version 2 of the D. biarmipes assembly. The output of the pipeline did not include the placement of the 454 and Illumina reads that were used to construct the consensus. As a first approximation, we mapped all the genomic reads against the...
by wleung
Tue Sep 23, 2014 3:25 pm
Forum: Sequence Improvement Questions
Topic: High number HQDs - only one run matches consensu
Replies: 5
Views: 8235

Re: High number HQDs - only one run matches consensus

We constructed the Consed assemblies by mapping the Illumina and 454 reads against the published consensus sequence. The protocol we used to create the ace file does not change the consensus because we would like the consensus for the Consed assembly to match the published assembly. This allows us t...
by wleung
Tue Sep 23, 2014 3:12 pm
Forum: Sequence Improvement Questions
Topic: PCR Primer Extraction
Replies: 2
Views: 6481

Re: PCR Primer Extraction

The name of the program is ace2Oligos.perl and the syntax for the command is as follow: ace2Oligos.perl <name of ace file> <name of oligos file> Therefore, you can use the following command to extract the oligos in DBIA1412001.ace.3: ace2Oligos.perl ./DBIA1412001.ace.3 ./pcr_primers.txt If the comma...
by wleung
Sat Aug 23, 2014 6:14 pm
Forum: GEP Web System Updates
Topic: Changes to the GEP Web Framework - Fall 2014
Replies: 0
Views: 9202

Changes to the GEP Web Framework - Fall 2014

Hello Everyone, We have reset the GEP Web Framework for the 2014 Fall semester. The list of key changes are summarized below: 1. Annotation and sequence improvement projects for Fall 2014 D. biarmipes Muller D element annotation projects (TSS annotations optional) D. biarmipes Muller F and D element...
by wleung
Mon Jul 14, 2014 7:43 pm
Forum: Sequence Improvement Questions
Topic: Maps of all Annotation and Finishing Projects
Replies: 1
Views: 5150

Re: Maps of all Annotation and Finishing Projects

The placement of the D. biarmipes F element projects are available on the GEP UCSC Genome Browser mirror under the April 2013 (BCM-HGSC) assembly. The placement of the annotation and finishing projects are available through the GEP V1 projects and Finishing Projects tracks respectively (under the "A...
by wleung
Fri Jun 13, 2014 6:06 am
Forum: Annotation Questions
Topic: Half of exons in another contig/should be reported?
Replies: 1
Views: 4910

Re: Half of exons in another contig/should be reported?

Your students are only responsible for annotating the set of complete exons of Asator in contig29. Please include a note in the Project Report indicating that the rest of the Asator gene is in contig28.
by wleung
Fri May 02, 2014 9:05 pm
Forum: Annotation Questions
Topic: Sequencing error?
Replies: 10
Views: 12234

Re: Sequencing error?

Per our previous discussions , the blastx track shows region of sequence similarity between the contig and a D. melanogaster protein. Consequently, your students should not use the blastx track to infer the gene structure. This is also one of the main reasons for performing the exon by exon searches...
by wleung
Fri May 02, 2014 5:09 am
Forum: Annotation Questions
Topic: Sequencing error?
Replies: 10
Views: 12234

Re: Sequencing error?

CDS 6_1774_0 (the initial coding exon of the B isoform of CG2219) likely does not exist in D. biarmipes . In D. melanogaster , CDS 6_1774_0 and 7_1762_0 overlap with each other and CDS 6_1774_0 has one extra amino acid near the splice donor site. Examination of the Conservation track shows that the ...
by wleung
Fri May 02, 2014 12:14 am
Forum: Annotation Questions
Topic: Sequencing error?
Replies: 10
Views: 12234

Re: Sequencing error?

I am not sure I understand the question. The blastx alignment for CDS 5_1762_0 ends at 20929 in frame -1. As shown in the screenshot below, there is a phase 0 splice donor site immediately upstream at 20928-20927. splice_donor_CDS_5_1762_0.png The blastx alignment for CDS 4_1762_0 begins at 20869 in...
by wleung
Wed Apr 30, 2014 12:16 am
Forum: Annotation Questions
Topic: Number of exons
Replies: 2
Views: 6484

Re: Number of exons

The blastx track on the genome browser shows the alignments between the D. melanogaster proteins and the contig sequence. The boxes in the blastx track correspond to regions of the contig that is similar to a D. melanogaster protein (i.e. an alignment block). In many cases, the alignment blocks woul...
by wleung
Thu Apr 24, 2014 10:47 pm
Forum: Annotation Questions
Topic: Annotate gene?
Replies: 1
Views: 5232

Re: Annotate gene?

Please add a note in the "Preparing the project for submission" section of the GEP Annotation Report indicating that the gene prediction most likely corresponds to a unmasked transposon fragment. The species-specific transposon library used by RepeatMasker is constructed by comparing the entire geno...
by wleung
Thu Apr 24, 2014 4:46 pm
Forum: Annotation Questions
Topic: New genes
Replies: 4
Views: 8012

Re: New genes

Yes, you can use " Dbia-GEP001-PA " as the gene name when verifying the gene model using the Gene Model Checker. However, in general, I would not annotate a feature as a gene unless the feature shows significant sequence similarity to another known gene in the NCBI nr protein database or contains a ...
by wleung
Wed Apr 23, 2014 4:54 am
Forum: Annotation Questions
Topic: New genes
Replies: 4
Views: 8012

Re: New genes

For novel genes that are not present in D. melanogaster , your student should enter the species and the ortholog name that was used to construct the gene model in the "Ortholog in D. melanogaster" field of the Gene Model Checker configuration form. For example the GEP has previously identified a nov...
by wleung
Thu Apr 10, 2014 11:22 pm
Forum: Annotation Questions
Topic: Exon location
Replies: 4
Views: 6438

Re: Exon location

The discrepancy is likely caused by a non-canonical GC splice donor site at the end of CDS 3_1762_0 According to the Gene Record Finder, both the CDS 3_1762_0 and 5_1762_2 have a non-canonical GC donor site in D. melanogaster . Consequently, if this CDS is conserved in D. biarmipes , we would look f...
by wleung
Thu Apr 10, 2014 4:26 am
Forum: Annotation Questions
Topic: Frame disagreement between browser and Blastx alignments
Replies: 4
Views: 6702

Re: Frame disagreement between browser and Blastx alignments

> My student was unable to open the sequence file in the src folder. The sequence file in the "src" folder is a plain text file so you can open the file in any text editor (e.g. WordPad on Windows and TextEdit on the Mac). You may need to manually select the program if the operating system does not ...