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ProphET
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gff_rewrite.pl stop in one place and don't move
#53
nienie123123
opened
1 year ago
0
Installation and running
#52
Songhaoqiu
opened
2 years ago
0
INSTALL.pl script error "cat:...No such file or directory"
#51
rorycave
opened
2 years ago
0
Running ProphET against multiple genomes
#50
JosephWestley
opened
3 years ago
0
Regarding attL and attR identification in predicted prophage sequence
#49
shakti83kumar
opened
3 years ago
0
GFF converter not working
#48
hayleyjaywilson
opened
3 years ago
0
GFF compatibility (Prooka output --compliant flag)
#47
nilesh-tawari
closed
3 years ago
1
Compatibility with Prokka generated GFF using (--compliant) option
#46
nilesh-tawari
opened
3 years ago
3
GFF format convert trouble
#45
PaolaLis8
closed
3 years ago
0
Unable to find the transcript and gene associated to the CDS
#44
stefjanson
closed
4 years ago
2
please provide a clean install
#43
phiweger
opened
4 years ago
4
What tool(s) from EMBOSS do you need?
#42
tseemann
opened
4 years ago
0
Missing description
#41
tseemann
opened
4 years ago
0
Deprecated database when using ./INSTALL.pl or ./INSTALL.pl --update_db_only
#40
gkapatai
opened
4 years ago
2
Update ProphET_standalone.pl to use RealBin
#39
microbioticajon
opened
4 years ago
4
GFFFile module
#38
mariemh23
opened
5 years ago
3
Update ProphET_standalone.pl RealBin
#37
microbioticajon
closed
2 years ago
0
Ideas for updating ProphET
#36
nickp60
opened
5 years ago
0
[WIP] Various Updates to ProphET
#35
nickp60
closed
5 years ago
0
Corrupt FASTA File during install
#34
Hana288
opened
5 years ago
3
blastall error
#33
yuq1993
opened
6 years ago
0
Issue near ORI
#32
gustavo11
opened
6 years ago
0
Consolidate input: both coding sequences and tRNA could only be provided as part of the same GFF file
#31
gustavo11
closed
6 years ago
0
Phage genome download from ncbi
#30
ovpop100
opened
6 years ago
5
Update only
#29
gustavo11
closed
6 years ago
0
Add to each phage db directory a file containing a summary of phage db stats
#28
gustavo11
closed
6 years ago
0
Consider maintaining a copy of all phage db that were used
#27
gustavo11
closed
6 years ago
0
Include in TravisCI a test for executions using tRNA as a separate file
#26
gustavo11
closed
6 years ago
1
Travis CI checks should be less stringent
#25
gustavo11
closed
6 years ago
1
Database updating
#24
kabilov
closed
6 years ago
3
Some of the log files are being saved in the base directory of execution and later copied to output dir
#23
gustavo11
opened
6 years ago
0
Adapt application to blast+
#22
gustavo11
opened
6 years ago
0
Github release
#21
Takadonet
closed
6 years ago
2
GFF format trouble
#20
mariemh23
opened
6 years ago
21
Could not find fetch_genomes_based_on_taxid.xml when running INSTALL.pl
#19
scottdaniel
closed
6 years ago
1
There are two points in the code where STOP codons are discarded. Remove redundancy.
#18
gustavo11
closed
6 years ago
1
ABC transporters are not being removed from ProphET database
#17
gustavo11
closed
7 years ago
0
Setting up travis CI
#16
gustavo11
closed
7 years ago
0
obtain_prot_with_annot_seq.pl seems to be unnecessary
#15
gustavo11
opened
7 years ago
0
Translate to english comments
#14
gustavo11
closed
7 years ago
0
To provide a more extensive description of the prophages found
#13
gustavo11
closed
7 years ago
1
To provide a better description of the files generated
#12
gustavo11
closed
6 years ago
1
Investigate the possibility of taking output of Prokka
#11
gustavo11
opened
7 years ago
7
Error on line 119 of INSTALL.pl
#10
gustavo11
closed
7 years ago
0
The script is considering part of GFF description as sequence ids
#9
gustavo11
closed
7 years ago
0
Include in the manual the format of GFF that should be used and how to convert to that format
#8
gustavo11
closed
6 years ago
0
Generate file reporting the day of Prophage database update and stats about that database
#7
gustavo11
closed
6 years ago
0
Output GFFs reporting prophage gene coordinates and annotation
#6
gustavo11
opened
7 years ago
0
Improve graph depicting genes, genomes and predicted prophage
#5
gustavo11
opened
7 years ago
0
Assign name to predicted phages
#4
gustavo11
opened
7 years ago
0
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