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Laurent Falquet
, …
Richel J.C. Bilderbeek
3
5/11/20
prodigal web server down?
Still down as of 11/05/2020. Any news? On Friday, January 19, 2018 at 7:25:05 PM UTC+1, Eric Deveaud
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prodigal web server down?
Still down as of 11/05/2020. Any news? On Friday, January 19, 2018 at 7:25:05 PM UTC+1, Eric Deveaud
5/11/20
rudype...@gmail.com
, …
Jianshu Zhao
3
5/1/20
Multithreading
Hi Doug, Any idea where I can find the python wrapper of multiprocess prodigal? I guess there must be
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Multithreading
Hi Doug, Any idea where I can find the python wrapper of multiprocess prodigal? I guess there must be
5/1/20
jigyasa arora
5/23/19
percent of genes predicted
Is it possible to do something like- (no.of protein-coding genes/no.of contigs in a metagenome) = to
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percent of genes predicted
Is it possible to do something like- (no.of protein-coding genes/no.of contigs in a metagenome) = to
5/23/19
Erica Lasek-Nesselquist
3/6/18
cannot specify genetic code 29
Dear Doug, I'm wondering if there is anyway that Prodigal will recognize genetic code 29 (
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cannot specify genetic code 29
Dear Doug, I'm wondering if there is anyway that Prodigal will recognize genetic code 29 (
3/6/18
FPO
12/20/17
Understanding 'partial' field in the Prodigal output
Hi, Prodigal predicted the following gene on the reverse strand of the edge of a contig. The contig
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Understanding 'partial' field in the Prodigal output
Hi, Prodigal predicted the following gene on the reverse strand of the edge of a contig. The contig
12/20/17
a...@secondgenome.com
,
Doug Hyatt
2
11/1/17
Comparing outputs from different runs on same dataset.
Not sure I'm following. If you run prodigal multiple times on the same input file, you should get
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Comparing outputs from different runs on same dataset.
Not sure I'm following. If you run prodigal multiple times on the same input file, you should get
11/1/17
Furqan Awan
,
dhyatt1
2
9/7/17
How to install this on Windows 7?
There is no true windowed version of Prodigal. The Windows binary is just a command-line tool. You
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How to install this on Windows 7?
There is no true windowed version of Prodigal. The Windows binary is just a command-line tool. You
9/7/17
Kecen Zhou
,
dhyatt1
2
9/7/17
How do you install on Mac?
The macosx file is a binary. You can rename it to "prodigal" with mv, chmod if it isn't
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How do you install on Mac?
The macosx file is a binary. You can rename it to "prodigal" with mv, chmod if it isn't
9/7/17
Nausheen Fatima
8/11/17
newbie here
I'm very new to command line and trying to extract ORFs from prodigal for some plasmid seqs. Can
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newbie here
I'm very new to command line and trying to extract ORFs from prodigal for some plasmid seqs. Can
8/11/17
Indugu Nagaraju
8/9/17
difference in number of sequences in Protein Translations and Nucleotide Sequences
Hi Prodigal discussion group I have used Prodigal to see the protein coding genes in the meta-
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difference in number of sequences in Protein Translations and Nucleotide Sequences
Hi Prodigal discussion group I have used Prodigal to see the protein coding genes in the meta-
8/9/17
alien zj
6/14/17
Can prpdigal only translate the predicted gene sequence?
Hello, everyone! Is this, I used idba to assembly many sample's raw data, and got a lot of
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Can prpdigal only translate the predicted gene sequence?
Hello, everyone! Is this, I used idba to assembly many sample's raw data, and got a lot of
6/14/17
Luca Venturini
,
dhyatt1
2
3/10/17
Use Prodigal to predict CDS sequences in *eukaryotic* transcriptomic sequences
You would have problems in anonymous/metagenomic mode because it will predict GTG and TTG starts. My
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Use Prodigal to predict CDS sequences in *eukaryotic* transcriptomic sequences
You would have problems in anonymous/metagenomic mode because it will predict GTG and TTG starts. My
3/10/17
Apiwat Sangphukieo
,
dhyatt1
2
3/10/17
Circular chromosome of completed genome
No, it does not have any flag for circular chromosomes. Most people who assemble genomes just
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Circular chromosome of completed genome
No, it does not have any flag for circular chromosomes. Most people who assemble genomes just
3/10/17
adithi r v
,
Doug Hyatt
2
9/16/16
Including CDS that overlaps with RNA
Prodigal doesn't predict or do anything with RNA genes. You may be thinking of Prokka or some
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Including CDS that overlaps with RNA
Prodigal doesn't predict or do anything with RNA genes. You may be thinking of Prokka or some
9/16/16
hila
9/16/16
minimum gene size
Hi, If I understand correctly, the minimum gene size that can be predicted by Prodigal is 90bp long.
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minimum gene size
Hi, If I understand correctly, the minimum gene size that can be predicted by Prodigal is 90bp long.
9/16/16
Jincheng Wang
5/26/16
Prodigal Amino Acid sequence
Dear Prodigal community, Hello! I have a question regarding to the Prodigal AA sequences. I was
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Prodigal Amino Acid sequence
Dear Prodigal community, Hello! I have a question regarding to the Prodigal AA sequences. I was
5/26/16
Brandon Kieft
,
Doug Hyatt
2
5/16/16
Why does Prodigal output "X" characters in predicted protein-coding sequences?
Prodigal's protein translation routine translates any codons with an ambiguous character in them
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Why does Prodigal output "X" characters in predicted protein-coding sequences?
Prodigal's protein translation routine translates any codons with an ambiguous character in them
5/16/16
Rob Bierman
,
dhyatt1
3
4/15/16
Valine and Leucine Start Amino Acids
Thanks for the quick reply Doug, that explains the V's and L's. My guess would be the same as
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Valine and Leucine Start Amino Acids
Thanks for the quick reply Doug, that explains the V's and L's. My guess would be the same as
4/15/16
SAMIK BAGCHI
,
dhyatt1
2
4/15/16
Visualize Prodigal output
This is more a question for Google (ie googling "visualize gff files" gives good results).
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Visualize Prodigal output
This is more a question for Google (ie googling "visualize gff files" gives good results).
4/15/16
zech xu
,
dhyatt1
2
4/15/16
prodigal version 3
No, not yet. When I wrote the wiki, I was hoping to have it out quickly. But my job changed (shortly
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prodigal version 3
No, not yet. When I wrote the wiki, I was hoping to have it out quickly. But my job changed (shortly
4/15/16
klmb...@gmail.com
,
dhyatt1
2
12/30/15
gbk and gff outputs at the same time?
This is not currently an available option, but if it's something more users want, I could
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gbk and gff outputs at the same time?
This is not currently an available option, but if it's something more users want, I could
12/30/15
Vivek Keshri
,
dhyatt1
2
12/30/15
About Translation Table
This is not currently possible, since metagenome mode uses preset training files (none of which use
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About Translation Table
This is not currently possible, since metagenome mode uses preset training files (none of which use
12/30/15
Emma Timmins-Schiffman
,
Doug Hyatt
2
12/30/15
Invalid meta/single genome type specified.
Hi, The wiki currently references a future version of Prodigal (3.0), which will use that syntax. For
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Invalid meta/single genome type specified.
Hi, The wiki currently references a future version of Prodigal (3.0), which will use that syntax. For
12/30/15
Nikunj Maheshwari
,
Doug Hyatt
2
3/5/15
Two different genomes in a single fasta file
Prodigal treats the contents of a FASTA file as a single genome. You should split your genomes into
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Two different genomes in a single fasta file
Prodigal treats the contents of a FASTA file as a single genome. You should split your genomes into
3/5/15
Erik Lysøe
,
dhyatt1
2
2/25/15
Bug report!
I am unable to reproduce this bug. It likely has something to do with the input sequence, so I would
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Bug report!
I am unable to reproduce this bug. It likely has something to do with the input sequence, so I would
2/25/15
periwa...@gmail.com
,
dhyatt1
2
1/21/15
gbProks-prodigal not updated?
I don't think I ever got around to finishing the script to run Prodigal. GBProks is on hold at
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gbProks-prodigal not updated?
I don't think I ever got around to finishing the script to run Prodigal. GBProks is on hold at
1/21/15
jfchi...@gmail.com
,
dhyatt1
2
1/21/15
Access via Putty SSH?
Hi, I'm afraid I don't really understand the question. Prodigal is a single self-contained
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Access via Putty SSH?
Hi, I'm afraid I don't really understand the question. Prodigal is a single self-contained
1/21/15
Intikhab
,
dhyatt1
2
1/21/15
prodigal prediction frame
My understanding of the frame field in GFF is that it is supposed to report the reading frame of
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prodigal prediction frame
My understanding of the frame field in GFF is that it is supposed to report the reading frame of
1/21/15
Aurélie Génin Lajus
,
dhyatt1
2
1/21/15
Codon Usage 25 for bacteria
Hi, I've added support for translation table 25 to the latest source commit at github. Going to
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Codon Usage 25 for bacteria
Hi, I've added support for translation table 25 to the latest source commit at github. Going to
1/21/15
shaun...@phac-aspc.gc.ca
, …
Doug Hyatt
8
10/7/14
Bug report ???
Sorry I did do that but I'm still confused. But maybe I just don't understand the scoring.
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Bug report ???
Sorry I did do that but I'm still confused. But maybe I just don't understand the scoring.
10/7/14