SEA-PHAGES | Whole-genome amino acid sequences were obtained from Phamerator

Link to this post \| posted 06 May, 2016 18:02
GregFrederick@letu.edu	In this paper, "Whole-genome amino acid sequences were obtained from The Genomes, Proteomes, and Structures of Three Novel Phages That Infect the Bacillus cereus Group and Carry Putative Virulence Factors" by Julianne H. Grose,a David M. Belnap,b Jordan D. Jensen,a Andrew D. Mathis,c John T. Prince,c Bryan D. Merrill,a Sandra H. Burnett,a Donald P. Breakwella….. They do a dot-plot analysis of several phage genomes with GEPARD. They do both nucleotide and Amino Acid comparisons. QUESTION: In the legend of the figure showing the dot plots, they state "Whole-genome amino acid sequences were obtained from Phamerator". I cannot see how to get whole genome amino acid sequences out of Phamerator. I know how to get single gene AA sequences. How does one extract 'whole-genome amino acid sequences from Phamerator? Clues? Thanks in advance. Greg

Link to this post | posted 06 May, 2016 18:02

In this paper, "Whole-genome amino acid sequences were obtained from The Genomes, Proteomes, and Structures of Three Novel Phages That Infect the Bacillus cereus Group and Carry Putative Virulence Factors" by Julianne H. Grose,a David M. Belnap,b Jordan D. Jensen,a Andrew D. Mathis,c John T. Prince,c Bryan D. Merrill,a Sandra H. Burnett,a
Donald P. Breakwella…..

They do a dot-plot analysis of several phage genomes with GEPARD. They do both nucleotide and Amino Acid comparisons.

QUESTION: In the legend of the figure showing the dot plots, they state "Whole-genome amino acid sequences were obtained from Phamerator". I cannot see how to get whole genome amino acid sequences out of Phamerator. I know how to get single gene AA sequences. How does one extract 'whole-genome amino acid sequences from Phamerator? Clues?

Thanks in advance. Greg

Link to this post \| posted 16 May, 2016 15:18
cdshaffer	in phamerator select "Phages" in left column, then select the phage you want. Then in the magic appearing menu at the top select File -> Export Proteins (fasta) save the file, it is a text based multi-fasta file which you can open with any text editor to view and load into GEPARD for dotplot. You can also get all proteins sequences for any phage in GenBank: go to genbank record (easy from phagesdb phage page), in upper right corner click "Send", then select Coding sequences, then pick if you want the sequences as nucleotide or amino acids. The downloaded file will also contain all the gene sequences as a text file. Very similar to the file from phamerator but with a lot more info in the header line for each gene which can either be useful if you need any of that info or just in the way if you don't

Link to this post | posted 16 May, 2016 15:18

cdshaffer

in phamerator select "Phages" in left column, then select the phage you want.
Then in the magic appearing menu at the top select File -> Export Proteins (fasta)

save the file, it is a text based multi-fasta file which you can open with any text editor to view and load into GEPARD for dotplot.

You can also get all proteins sequences for any phage in GenBank: go to genbank record (easy from phagesdb phage page), in upper right corner click "Send", then select Coding sequences, then pick if you want the sequences as nucleotide or amino acids. The downloaded file will also contain all the gene sequences as a text file. Very similar to the file from phamerator but with a lot more info in the header line for each gene which can either be useful if you need any of that info or just in the way if you don't

Link to this post \| posted 16 May, 2016 18:55
GregFrederick@letu.edu	Super. I appreciate the response. Lee Hughes gave me the same info outside the forum. (We are in the same ASM branch… I should have updated the thread. Much appreciated. GF

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Whole-genome amino acid sequences were obtained from Phamerator