SEA-PHAGES | All posts created by gissendanner

Link to this post \| posted 03 Jul, 2018 19:53
gissendanner	In Sombrero, I have found a couple of genes where there is a TTG start followed by ATG. Glimmer and GeneMark both pick the ATG as the start. The same genes in other CS2 phage have mostly been annotated with the TTG start. The RBS Z-score is the same for both but the final score goes down a little for the TTG start. Given that TTG is rarely used, is it correct to assign TTG as the start in this situation?

Link to this post | posted 03 Jul, 2018 19:53

In Sombrero, I have found a couple of genes where there is a TTG start followed by ATG. Glimmer and GeneMark both pick the ATG as the start. The same genes in other CS2 phage have mostly been annotated with the TTG start. The RBS Z-score is the same for both but the final score goes down a little for the TTG start. Given that TTG is rarely used, is it correct to assign TTG as the start in this situation?

Posted in: Cluster CS Annotation Tips → TTG followed by ATG

Link to this post \| posted 02 Jul, 2018 02:08
gissendanner	After further analysis, GP2 is not well supported to be a small terminase subunit, other than the blast hit to Nyceirae where the same gene is annotated as a small terminase subunit. Both GP3 and GP4 have good support as a large subunit, both from HHpred and Phyre2. Interestingly, GP3 has a coiled-coil domain which is typically found in the small subunit. So, I do not see a small subunit gene and possibly two large subunit genes. Any guidance on the best annotation approach here?

Link to this post | posted 02 Jul, 2018 02:08

gissendanner

After further analysis, GP2 is not well supported to be a small terminase subunit, other than the blast hit to Nyceirae where the same gene is annotated as a small terminase subunit. Both GP3 and GP4 have good support as a large subunit, both from HHpred and Phyre2. Interestingly, GP3 has a coiled-coil domain which is typically found in the small subunit. So, I do not see a small subunit gene and possibly two large subunit genes. Any guidance on the best annotation approach here?

Posted in: Cluster DT Annotation Tips → Terminase Genes

Link to this post \| posted 01 Jul, 2018 23:10
gissendanner	According to the bioinformatics guide, there should no more than two terminase genes in the genome–minor subunit and major subunit. Dogfish appears to have three. GP2 is a small subunit gene and GP3 and GP4 appear to be large subunit genes supported by both BLAST and HHPred. This region also has synteny with Nyceirae and Nyceirae is also annotated to have two large terminase subunit genes (3 terminase genes total). Should Dogfish be annotated to have three terminase genes? Thanks Chris

Link to this post | posted 01 Jul, 2018 23:10

gissendanner

According to the bioinformatics guide, there should no more than two terminase genes in the genome–minor subunit and major subunit. Dogfish appears to have three. GP2 is a small subunit gene and GP3 and GP4 appear to be large subunit genes supported by both BLAST and HHPred. This region also has synteny with Nyceirae and Nyceirae is also annotated to have two large terminase subunit genes (3 terminase genes total). Should Dogfish be annotated to have three terminase genes?

Thanks
Chris

Posted in: Cluster DT Annotation Tips → Terminase Genes

Link to this post \| posted 01 Jul, 2018 23:00
gissendanner	In Dogfish, there appears to be a slippery sequence starting at base 11314 at the end of GP 17 and beginning of GP 18. At 11317 there would be a -1 frameshift. Nyceirae also this slippery sequence and sequence identity in the region. However, a frameshift is not annotated. Should I include this frameshift for Dogfish, or annotate the same as Nyceirae? Thanks Chris

Posted in: Cluster DT Annotation Tips → Tail assembly chaperones?

Link to this post \| posted 21 Jun, 2018 16:29
gissendanner	GP32 PHAM in Catfish (Draft) is also found in Vendetta (GP32) the closest related phage to Catfish. Vendetta lists function as DNA binding protein. There is a good HHPred score to an excisionase. It seems that both could apply based on BLAST Hits. Excise is an approved function, so which to use, excise or DNA binding protein? Or is hypothetical protein best. Thanks

Posted in: Singleton Annotation Tips → Excise or DNA binding protein?

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