SEA-PHAGES | BLASTing whole genome with "secure" connection

BLASTing whole genome with "secure" connection

Link to this post \| posted 07 Feb, 2017 15:01
jross1025	Yesterday about 4 I started a BLAST-all-genes for our L cluster guy using the updated DNA Master with the secure NCBI connections–first time I've done this since the update. Result was very spotty–lots of genes skipped. Right now I'm doing "BLAST this gene" one at a time, which seems to be doing fine, but that's a pain. Should I have waited till late at night or on the weekend? Also I'm seeing something now in one gene that I've only ever seen in HHPred, not in BLAST: E values greater than 1. If this is really a mathematical probability, how is that possible? Is it just BLAST's way of saying "this is a crummy hit (which it was)"?

Link to this post | posted 07 Feb, 2017 15:01

Yesterday about 4 I started a BLAST-all-genes for our L cluster guy using the updated DNA Master with the secure NCBI connections–first time I've done this since the update. Result was very spotty–lots of genes skipped. Right now I'm doing "BLAST this gene" one at a time, which seems to be doing fine, but that's a pain. Should I have waited till late at night or on the weekend? Also I'm seeing something now in one gene that I've only ever seen in HHPred, not in BLAST: E values greater than 1. If this is really a mathematical probability, how is that possible? Is it just BLAST's way of saying "this is a crummy hit (which it was)"?

Link to this post \| posted 07 Feb, 2017 16:39
DanRussell	Hi Joe, As for the BLASTing, you could try an intermediate approach between all-genes and one-at-a-time. Welkin made a video about how to BLAST a batch of genes in DNA Master, so you could try chunks of 10 for example. Batch BLASTing in DNA Master As to the E-value, those might just be a result of having a less-common cluster of phage this time around. If you had a new Singleton, you'd expect to see some genes with not-good BLAST hits. Cluster L3s are not that common (only 4 in GenBank, I believe), so it's totally possible that those are "new" genes. Check them out in Phamerator and see if they're orphams. (And an e-value of 1 just means that you'd expect about 1 hit this good against a database this size by random chance…meaning it is indeed a dubious result.) –Dan

Link to this post | posted 07 Feb, 2017 16:39

DanRussell

Hi Joe,

As for the BLASTing, you could try an intermediate approach between all-genes and one-at-a-time. Welkin made a video about how to BLAST a batch of genes in DNA Master, so you could try chunks of 10 for example.

Batch BLASTing in DNA Master

As to the E-value, those might just be a result of having a less-common cluster of phage this time around. If you had a new Singleton, you'd expect to see some genes with not-good BLAST hits. Cluster L3s are not that common (only 4 in GenBank, I believe), so it's totally possible that those are "new" genes. Check them out in Phamerator and see if they're orphams.

(And an e-value of 1 just means that you'd expect about 1 hit this good against a database this size by random chance…meaning it is indeed a dubious result.)

–Dan

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BLASTing whole genome with "secure" connection