SEA-PHAGES | All posts created by nietof

Link to this post \| posted 09 Mar, 2020 17:58
nietof	Hi What is the best way for downloading fasta files for a selected group of phages to build phylogenetic trees? I downloaded the complete fasta file from phagesdb and then I searched the sequences using the phage names, but it takes forever for large clusters like A1. Thank you Fernando

Posted in: Phage Biology → Downloading cluster specific fasta files

Link to this post \| posted 21 Jan, 2020 16:00
nietof	Hi Dan I am using a school laptop from home, the laptop was initially set up by our IT. I am working using an administrator account. I found a post on DNA Master and Windows 10 from Welkin dealing with the Windows 10 UAC. I follow her instructions to add DNA Master as a trusted application in windows 10. I reinstalled DNA Master. Let's see how long it works. Thank you F

Posted in: DNA Master → DNA Master Issue

Link to this post \| posted 21 Jan, 2020 14:52
nietof	Hi I installed DNA Master in a PC with windows 10. It works fine for a while then it doesn't find the path and the application doesn't open up at all. The icon in the desktop appears white. When I try to open the application from the actual folder where it is installed, the DNAMas icon also appears white and it gives me the following error: "Windows cannot access the specified device, path, or file. You may not have the appropriate permissions to access the item". This is the second time it happens. The first time I uninstalled it and install it again. Any clues? thanks Fernando

Link to this post | posted 21 Jan, 2020 14:52

nietof

Hi
I installed DNA Master in a PC with windows 10. It works fine for a while then it doesn't find the path and the application doesn't open up at all. The icon in the desktop appears white. When I try to open the application from the actual folder where it is installed, the DNAMas icon also appears white and it gives me the following error: "Windows cannot access the specified device, path, or file. You may not have the appropriate permissions to access the item". This is the second time it happens. The first time I uninstalled it and install it again. Any clues?
thanks
Fernando

Posted in: DNA Master → DNA Master Issue

Link to this post \| posted 05 Dec, 2019 21:52
nietof	Not sure why the smiley appears there the error number is 2108. thanks F

Posted in: DNA Master → TbQueries

Link to this post \| posted 05 Dec, 2019 21:44
nietof	Hi All of a sudden today I am getting an error when I open DNA Master "Queries table is corrupt. Reload from FTP DNA Master FTP site. When I try to reload from FTP site it gives me a second error "An error occurred when attempting to initialize the Borland Database Engine (Error $210". Any helps is appreciated. Fernando

Posted in: DNA Master → TbQueries

Link to this post \| posted 03 Jun, 2019 19:00
nietof	Welkin Here is the other orpham gene 58 in phamerator (gene 57 in DNA Master). This gene is called by Glimmer not by GeneMark but with strong CP in GeneMarkS. There is no functional assignment in BlastP and poor hits in HHPred, smallest E value is 31. We are inclined not to call it either. It is in the forward strand but all the genes in that region of the genome are on the reverse strand. Fernando 69Kb

Link to this post | posted 03 Jun, 2019 19:00

nietof

Welkin
Here is the other orpham gene 58 in phamerator (gene 57 in DNA Master). This gene is called by Glimmer not by GeneMark but with strong CP in GeneMarkS. There is no functional assignment in BlastP and poor hits in HHPred, smallest E value is 31. We are inclined not to call it either. It is in the forward strand but all the genes in that region of the genome are on the reverse strand.
Fernando

Posted in: Gene or not a Gene → question on orpham gene on forward strand of Snazzy

Link to this post \| posted 03 Jun, 2019 16:16
nietof	nietof nietof Hi Snazzy Gene 58 in phamerator is called as a forward gene overlapping with gene 57 a reverse gnee in a section of the genome where all the genes are coded on the reverse strand. Glimmer calls it in DNA Master but as gene 57 (difference in gene numbers between phagesDB/phamerator and DNA master is due to another questionable orpham gene 35 called only in PhagesDB/phamerator, but not called by Glimmer in DNA Master and with very poor CP in GeneMarkS). Gene 57 is called by Glimmer not by GeneMark but with strong CP in GeneMarkS. There is no functional assignment in BlastP and poor hits in HHPred, smallest E value is 31. We are inclined not to call either one of these orpham genes. Fernando Sorry, here is orpham gene 35 in phamerator. F 59Kb

Link to this post | posted 03 Jun, 2019 16:16

nietof

nietof
nietof
Hi
Snazzy Gene 58 in phamerator is called as a forward gene overlapping with gene 57 a reverse gnee in a section of the genome where all the genes are coded on the reverse strand. Glimmer calls it in DNA Master but as gene 57 (difference in gene numbers between phagesDB/phamerator and DNA master is due to another questionable orpham gene 35 called only in PhagesDB/phamerator, but not called by Glimmer in DNA Master and with very poor CP in GeneMarkS). Gene 57 is called by Glimmer not by GeneMark but with strong CP in GeneMarkS. There is no functional assignment in BlastP and poor hits in HHPred, smallest E value is 31. We are inclined not to call either one of these orpham genes.
Fernando

Sorry, here is orpham gene 35 in phamerator.
F

Posted in: Gene or not a Gene → question on orpham gene on forward strand of Snazzy

Link to this post \| posted 03 Jun, 2019 16:15
nietof	nietof Hi Snazzy Gene 58 in phamerator is called as a forward gene overlapping with gene 57 a reverse gnee in a section of the genome where all the genes are coded on the reverse strand. Glimmer calls it in DNA Master but as gene 57 (difference in gene numbers between phagesDB/phamerator and DNA master is due to another questionable orpham gene 35 called only in PhagesDB/phamerator, but not called by Glimmer in DNA Master and with very poor CP in GeneMarkS). Gene 57 is called by Glimmer not by GeneMark but with strong CP in GeneMarkS. There is no functional assignment in BlastP and poor hits in HHPred, smallest E value is 31. We are inclined not to call either one of these orpham genes. Fernando 66Kb

Link to this post | posted 03 Jun, 2019 16:15

nietof

nietof
Hi
Snazzy Gene 58 in phamerator is called as a forward gene overlapping with gene 57 a reverse gnee in a section of the genome where all the genes are coded on the reverse strand. Glimmer calls it in DNA Master but as gene 57 (difference in gene numbers between phagesDB/phamerator and DNA master is due to another questionable orpham gene 35 called only in PhagesDB/phamerator, but not called by Glimmer in DNA Master and with very poor CP in GeneMarkS). Gene 57 is called by Glimmer not by GeneMark but with strong CP in GeneMarkS. There is no functional assignment in BlastP and poor hits in HHPred, smallest E value is 31. We are inclined not to call either one of these orpham genes.
Fernando

Posted in: Gene or not a Gene → question on orpham gene on forward strand of Snazzy

Link to this post \| posted 03 Jun, 2019 16:15
nietof	Hi Snazzy Gene 58 in phamerator is called as a forward gene overlapping with gene 57 a reverse gnee in a section of the genome where all the genes are coded on the reverse strand. Glimmer calls it in DNA Master but as gene 57 (difference in gene numbers between phagesDB/phamerator and DNA master is due to another questionable orpham gene 35 called only in PhagesDB/phamerator, but not called by Glimmer in DNA Master and with very poor CP in GeneMarkS). Gene 57 is called by Glimmer not by GeneMark but with strong CP in GeneMarkS. There is no functional assignment in BlastP and poor hits in HHPred, smallest E value is 31. We are inclined not to call either one of these orpham genes. Fernando

Link to this post | posted 03 Jun, 2019 16:15

nietof

Hi
Snazzy Gene 58 in phamerator is called as a forward gene overlapping with gene 57 a reverse gnee in a section of the genome where all the genes are coded on the reverse strand. Glimmer calls it in DNA Master but as gene 57 (difference in gene numbers between phagesDB/phamerator and DNA master is due to another questionable orpham gene 35 called only in PhagesDB/phamerator, but not called by Glimmer in DNA Master and with very poor CP in GeneMarkS). Gene 57 is called by Glimmer not by GeneMark but with strong CP in GeneMarkS. There is no functional assignment in BlastP and poor hits in HHPred, smallest E value is 31. We are inclined not to call either one of these orpham genes.
Fernando

Posted in: Gene or not a Gene → question on orpham gene on forward strand of Snazzy

Link to this post \| posted 28 May, 2019 14:47
nietof	Debbie Somehow I had a misconception that a shift between 1 and 3 frames required a two base shift either back or forth(-2 or +2). It took me looking at the closely related genomes to realize that I was wrong. So I think I just needed confirmation on this one. Thank you. F

Posted in: Frameshifts and Introns → Help with frameshift annotation in A1 phage

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