User: allyson1115ar
allyson1115ar • 20
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- 3 years, 10 months ago
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- 5 years, 5 months ago
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Posts by allyson1115ar
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... This is indeed very helpful. Thanks. ...
written 4.0 years ago by
allyson1115ar • 20
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... How can I slice DNA sequence whenever NNN occurs and also letters that represent ambiguity? is there any available software tools I can use to do so?
For example:
'>chr1:0-45
ATCGCTAGCTAGCTRCGAGCGTAGCNNNNNNCGATCGATCGATCAG
into
'>chr1:0-13
ATCGCTAGCTAGCT
'>chr1:15-24
CGAGCGTAGC
' ...
written 4.0 years ago by
allyson1115ar • 20
• updated
3.2 years ago by
Biostar ♦♦ 20
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... I would like to know how to write the command that takes multiple gmhmm mod file in maker? An example of command that takes a single mod file is as such:
gmhmm=../train_genemark/es.mod #GeneMark HMM file
According to this link: http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/The_MAKER_con ...
written 4.2 years ago by
allyson1115ar • 20
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... the 3 species in my question ...
written 4.3 years ago by
allyson1115ar • 20
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... i would like to include the hmm in snap ab initio gene predictor since the package doesn't provide the other species ...
written 4.3 years ago by
allyson1115ar • 20
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... I can't find any hmm link to download the above 3 species :/ ...
written 4.3 years ago by
allyson1115ar • 20
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... I would like to ask is there any database allow me to download HMM for different species such as:
1. Pan troglodytes
2. Pongo abelii
3. Rhinopithecus rexellana ...
written 4.3 years ago by
allyson1115ar • 20
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... After I clicked 'full dataset', the only way for me to get hg18.fa is by downloading hg18.2bit and use twoBitToFa to convert to hg18.fa right? is there any link allow me to straight away download the hg18.fa without doing the conversion from twoBitToFa? thanks for your advice ...
written 4.4 years ago by
allyson1115ar • 20
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... In UCSC genome browser, the hg18 provided is not in one fasta file. They provide file to download for each chromosomes. May I know where can I download a hg18 complete fasta file that include all chromosomes? Thanks. ...
written 4.4 years ago by
allyson1115ar • 20
• updated
4.4 years ago by
Selenocysteine • 600
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... I have H3K4me1 bed file that I would like to obtain its sequence using UCSC genome browser. There are many options provided. I'm using the following options:
clade: mammal,
genome: human,
assembly: hg18,
group: ?,
track: ?
May I know what should I select for the group and track options? thanks. ...
written 4.4 years ago by
allyson1115ar • 20
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