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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...

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...

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...

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...

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...

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.

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...

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 ...

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...

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...

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...

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 ...

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...

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...

> 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 ...