Search found 13 matches

by pgupta
Mon May 13, 2013 10:58 pm
Forum: Annotation Questions
Topic: claimed same project twice...
Replies: 2
Views: 5797

Re: claimed same project twice...

Thanks!!
by pgupta
Mon May 13, 2013 8:46 pm
Forum: Annotation Questions
Topic: claimed same project twice...
Replies: 2
Views: 5797

claimed same project twice...

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
by pgupta
Thu May 02, 2013 3:40 pm
Forum: Annotation Questions
Topic: aanotation query for gene missing both 3' and 5' end
Replies: 1
Views: 4218

aanotation query for gene missing both 3' and 5' end

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...
by pgupta
Thu Apr 18, 2013 8:54 pm
Forum: Annotation Questions
Topic: Gene aligned using BlastX not present on desired chromosome?
Replies: 1
Views: 3998

Gene aligned using BlastX not present on desired chromosome?

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...
by pgupta
Mon Apr 15, 2013 5:04 pm
Forum: Annotation Questions
Topic: query regarding annotation word doc
Replies: 1
Views: 5385

query regarding annotation word doc

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
by pgupta
Thu Apr 11, 2013 7:06 pm
Forum: Annotation Questions
Topic: Query regarding PROJECT SUBMISSION..
Replies: 1
Views: 4611

Query regarding PROJECT SUBMISSION..

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...
by pgupta
Thu Apr 04, 2013 3:59 pm
Forum: Annotation Questions
Topic: query regarding annotation submission report
Replies: 1
Views: 4070

query regarding annotation submission report

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...
by pgupta
Thu Mar 21, 2013 8:04 pm
Forum: Annotation Questions
Topic: Same gene present on two different fosmids
Replies: 1
Views: 4060

Same gene present on two different fosmids

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 ...
by pgupta
Sat Feb 16, 2013 4:18 am
Forum: Annotation Questions
Topic: Problem in annotating D.ananassae fosmid
Replies: 4
Views: 6364

Re: Problem in annotating D.ananassae fosmid

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 ...
by pgupta
Thu Feb 14, 2013 8:57 pm
Forum: Annotation Questions
Topic: Problem in annotating D.ananassae fosmid
Replies: 4
Views: 6364

Problem in annotating D.ananassae fosmid

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...
by pgupta
Mon Jan 21, 2013 6:48 am
Forum: Annotation Questions
Topic: Query regarding D ananassae projects
Replies: 1
Views: 4664

Query regarding D ananassae projects

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...
by pgupta
Thu Aug 30, 2012 7:31 pm
Forum: Annotation Questions
Topic: last codon codes just for a stop codon
Replies: 1
Views: 3995

last codon codes just for a stop codon

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...