User: rh5118

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rh511820
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Location:
London, UK
Last seen:
1 year, 4 months ago
Joined:
2 years, 5 months ago
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h*********@gmail.com

PhD at the London School of Hygiene & Tropical Medicine working on molecular biology of the P falciparum malaria parasite. 

Posts by rh5118

<prev • 7 results • page 1 of 1 • next >
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Database searchingPKL Micromass File?
... Hi BioStars- Anyone have a good way of doing a database search on a PKL file? I need to search the mass spec data against a supplied proteome. I'd like to use Galaxy but I need to convert PKL to MGF, which I also don't know how to do. Many thanks! - A mass spec newbie ...
proteomics mass spec lc-ms ms written 19 months ago by rh511820 • updated 19 months ago by mobiusklein160
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Comment: C: Reannotating a gene: Identifying translation and transcription start sites
... Simply pick a suitable PAM site as close to the STOP codon as possible (unfortunately for me this was about 200 bp away) and then design a repair template to silently recodonise the CDS between the cut site and the STOP with a 3xHA tag stuck on the end of the CDS. You flank your changes (in this cas ...
written 2.5 years ago by rh511820
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Comment: C: Reannotating a gene: Identifying translation and transcription start sites
... Good one! Theoretically I could do it, but what an expensive mess that would be ...
written 2.5 years ago by rh511820
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Comment: C: Reannotating a gene: Identifying translation and transcription start sites
... Both really - as Michael points out (and in his comment below), it's probably technically easier to do RACE-PCR to figure out the full length transcript and then take the longest ORF. At least this will validate the splicing variation or genome misannotation theory. I can do a simple RT-PCR across t ...
written 2.5 years ago by rh511820
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Comment: C: Reannotating a gene: Identifying translation and transcription start sites
... Thanks - unfortunately you're probably right. It's a good idea to have in my back pocket if needed, but it's technically beyond what I would like to do as a first approach ...
written 2.5 years ago by rh511820
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Comment: C: Reannotating a gene: Identifying translation and transcription start sites
... Thanks for this suggestion. Do you know if this technique is going to be limited by transcript size? While I can make a guess at which Met is the start codon, I could certainly be wrong and the possibly transcript length for 5' RACE-PCR would be much longer. My thinking is that I can design it so I ...
written 2.5 years ago by rh511820
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Reannotating a gene: Identifying translation and transcription start sites
... Hi all - I'm working on a particular gene in Plasmodium falciparum that I have recently shown is misannotated in the reference genome. The current annotation shows that the gene has three exons; however, our recent data suggests that "exon 1" is not transcribed and spliced with exons 2 and/or 3. Th ...
genome gene rna-seq written 2.5 years ago by rh511820

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