SEA-PHAGES | Intergenic Repeated Sequences

Link to this post \| posted 09 May, 2022 16:00
Pollenz	In the DJ phages (and also in many of the Gordonia clusters) there is evidence for numerous intergenic 50-75bp repeated sequence are are located directly upstearm of the ATG start sites for 7-10 genes in the middle of the genome, (in the DJ the area is just upstream of the tape measure gene). Note that these areas are easily identified when looking at the Phamerator maps as solid lines that diverge to numerous areas and hit the genome UPSTREAM of numerous genes. The nature of the sequence can be found using the SCAN function in DNA master and also using programs like CLUSTAL OMEGA to identify the alignments. They key is that although gaps of 50-75bp between genes are atypical, in some cases there are start sites that can be found within these regions that create longer ORFS. These longer starts should not be called and its important to assess both the Glimmer and Genmark calls as usually they are the correct start for these types of genes. In some cases the longer starts have been annotated and this creates confusion. RS Pollenz 1.31Mb

Link to this post | posted 09 May, 2022 16:00

In the DJ phages (and also in many of the Gordonia clusters) there is evidence for numerous intergenic 50-75bp repeated sequence are are located directly upstearm of the ATG start sites for 7-10 genes in the middle of the genome, (in the DJ the area is just upstream of the tape measure gene). Note that these areas are easily identified when looking at the Phamerator maps as solid lines that diverge to numerous areas and hit the genome UPSTREAM of numerous genes. The nature of the sequence can be found using the SCAN function in DNA master and also using programs like CLUSTAL OMEGA to identify the alignments. They key is that although gaps of 50-75bp between genes are atypical, in some cases there are start sites that can be found within these regions that create longer ORFS. These longer starts should not be called and its important to assess both the Glimmer and Genmark calls as usually they are the correct start for these types of genes. In some cases the longer starts have been annotated and this creates confusion.

RS Pollenz

Link to this post \| posted 10 May, 2022 13:59
mdgainey	Hi Rick, I am going to look into some of the these repeats with my students this summer. They also have a different repeat towards that middle of the genome where there are a lot of membrane proteins, and there are also a lot of gaps. You can also find them using MEME, and this generates a nice output to look at. I am going to give this another eyeball before I submit my final DJ annotation.

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Intergenic Repeated Sequences