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Thanks!!

Hi While claiming projects, there were two projects which I claimed twice for the lab by mistake. We submitted both of them once but the claim status still shows 2 more copies of those projects. Submitting the same projects again does not help rectify it.Do I just leave it as it is? Thanks Paromita

Hi We are working on a fosmid which contains only one exon for a gene with 15 isoforms. The isoforms have this exon at a different position on the gene in melanogaster according to the gene record finder but same position on the genome browser for ananassae when aligned using blastX. Although the co...

Hi One of the fosmids(fosmid_1779L23-D.ana) we are working on aligns a bunch of genes in blastX alignment region.A protein blast for one of the predicted genes in that region in flybase gives us a number of hits with good e-values.However, most of the genes that have good e values are present on X o...

Hi

The word doc for the annotation submission has 2 slots for student name and email. There are a few projects that we took up for our lab session which were worked upon by students in groups of 3 or 4. Are they supposed to mention all the names and emails for these projects?

Thanks
Paromita

Hi We are trying to complete the word document required for the project submission and had a quick question about the section where we try to make sure that we are not missing out any genes in the fosmid.So we take the predicted protein sequence for the predicted genes on the fosmid which do not ali...

Hi For the last section of the annotation report where we perform a BLASTP search using the predicted amino acid sequence against the non-redundant protein database (nr) for regions of the project with gene predictions that do not overlap with putative orthologs identified in the BLASTX track, we ge...

Hi We are working on this gene called olf413 and it has 2 identical isoforms.Two projects fosmid 1770P16 and fosmid_2594O08 have the same gene (olf413-PB and olf-PC for one and olf413-RB and olf413-RC for the other). One project gives blast alignments that do not match up with the browsers software ...

Thanks!!:)

Hi Thank you for the quick and very detailed response :) .We were trying to annotate the SPoCk gene. I just have one more question.As only half of the gene seem to be present on the fosmid can we use the gene checker model for this gene(as we do not have the stop-cordinates)? If not, then how do we ...

Hi We have started working on one of the D.ananassae projects for the lab and are encountering this one common problem while annotating different isoform of the same gene.Flybase blast using predicted protein sequence gives us 6 isoforms of the gene, each having different exon positions. These are t...

Hi I had a query regarding the D ananassae projects for Jan 2013. For a number of projects where genscan predicts say 4 genes and the RNA seq data shows a high signal in particular regions when the predicted protein sequence is blasted no significant hits are obtained. Also although genscan predicts...

Hi I am working with a gene whose ortholog has 9 predicted exons.However the last exon is three bases long and codes for the stop codon only.Since we need to specify the stop codon position separately I entered the positions for only 8 exons in the gene checker.I get a pass sign for all the exons bu...