SEA-PHAGES | one gene won't blast

Link to this post \| posted 01 Jun, 2021 03:14
kclifton	I am finishing an annotation for submission. We used PECAAN and I pulled in the data and parsed the file successfully. When I re-blasted the file, the BIG gene (Podoviridae, so not tape measure but hypothetical protein)will not blast. I get an error and no blast data for only this gene. I've tried blasting just the single gene. Error every time. BUT - when I first did the original blast, the gene blasted just fine. I have a new computer now, so if it's my computer I don't know what it might be. CPU usage is nowhere near maxed out. I checked my newer blasted genome for a different phage and the tape measure gene blasted just fine on this same computer, and it's a lager gene than the one I'm having trouble with. I checked the sequence, it's fine. I can copy and paste it from DNAMAster and blast directly and it works. PECAAN blasted it fine as well. So I tried an old file with no PECAAN data parsed into it, and it won't blast from that file either. I sent it to my colleague and she can't get any blast results for this gene, whether a single gene or whole genome blast. I'm going to bring a student laptop home tomorrow and try it on that. I don't know what else to do. This one thing is preventing me from submitting the annotation. Any suggestions are much appreciated. Kari

Link to this post | posted 01 Jun, 2021 03:14

I am finishing an annotation for submission. We used PECAAN and I pulled in the data and parsed the file successfully. When I re-blasted the file, the BIG gene (Podoviridae, so not tape measure but hypothetical protein)will not blast. I get an error and no blast data for only this gene. I've tried blasting just the single gene. Error every time. BUT - when I first did the original blast, the gene blasted just fine. I have a new computer now, so if it's my computer I don't know what it might be. CPU usage is nowhere near maxed out. I checked my newer blasted genome for a different phage and the tape measure gene blasted just fine on this same computer, and it's a lager gene than the one I'm having trouble with.

I checked the sequence, it's fine. I can copy and paste it from DNAMAster and blast directly and it works. PECAAN blasted it fine as well. So I tried an old file with no PECAAN data parsed into it, and it won't blast from that file either. I sent it to my colleague and she can't get any blast results for this gene, whether a single gene or whole genome blast. I'm going to bring a student laptop home tomorrow and try it on that. I don't know what else to do. This one thing is preventing me from submitting the annotation. Any suggestions are much appreciated.

Kari

Link to this post \| posted 01 Jun, 2021 10:32
debbie	Hi Kari, Short and repetitive sequences are the culprits; some of the default settings for QBlast are probably different might exclude too much. That would lead to a very high EValue threshold, so no Results. Very little in QBLAST is specified by the user. In order words, it is an internal DNA Master setting. Just note that DNA Master wouldn't Blast it on your cover sheet. Thanks, debbie

Link to this post \| posted 03 Jun, 2021 23:05
kclifton	Thank you Debbie! I appreciate the info, this was very frustrating. At least happy to know it's not something I did/did not do. Kari

Link to this post \| posted 03 Jun, 2021 23:14
debbie	You are welcome!

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one gene won't blast