User: Jacob
Jacob • 10
- Reputation:
- 10
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- New User
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- Last seen:
- 2 years, 1 month ago
- Joined:
- 2 years, 5 months ago
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Posts by Jacob
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... I want to find reliable sources that give me the generation time for multiple organisms.
This is the average time in years between a parent and it's offspring for an organism. It can also be the age at which an organism reproduces. ...
written 2.2 years ago by
Jacob • 10
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... clustalw < input.txt
Where input.txt is
1
file.txt
2
9
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^@
1
^@
^@
^@
X
^@
X
The ^@ is one character, not two. It works as the enter key. You can type it like this
1. vim input.txt
2. i #going into insertion mode within vim
...
written 2.2 years ago by
Jacob • 10
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... I'm running command line tblastx for some human genes as the query sequences against the human genome as the target sequence. Almost all the searches are returning a query cover (qcovhsp) of 33%. I'm thinking that it is no coincidence that amino acids are 3 nucleotides long and that my query covers ...
written 2.2 years ago by
Jacob • 10
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... I am trying to run the command line clustalw, but within a loop.
Because of this I want to be able to set all the parameters at the time of execution, I don't want to change the parameters manually while the program is running
Here is what I am running
clustalw
1. Sequence Input From Disc
...
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... I'm am using the needle command and would just like there to be no output to the terminal
For example this is what I run
needle -asequence seq1.fna -bsequence seq2.fna -gapopen 0 -gapextend 2 -outfile file.needle
Needleman-Wunsch global alignment of two sequences
And I would jus ...
written 2.2 years ago by
Jacob • 10
• updated
2.2 years ago by
Charles Plessy • 2.7k
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... No just if theres a program that can take in this data and decide the stage, because I'm worried about misclassifying the stage based on my level of understanding. ...
written 2.3 years ago by
Jacob • 10
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... I don't know what that means, I'm trying make an accurate estimate of tumour stage based on a bunch of other data I have so that I can compare patient data where tumour stage is know to other data where tumour stage is not known ...
written 2.3 years ago by
Jacob • 10
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... For template_type and template_length, this is all I can really find on them
-template_type
Discontiguous MegaBLAST template type
-template_length
Discontiguous MegaBLAST template length
I don't really know what they are though and I don't know what differences setting op ...
written 2.4 years ago by
Jacob • 10
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... I'm working with breast cancer data and have lots of patient information regarding the tumour size(in cm), the type of the tumour(invasive ductal carcinoma; invasive lobular carcinoma; inflammatory carcinoma), the presence of lymph node metastasis, age of the patient, etc. For some patients I have i ...
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... I'm performing blast searches with only exon regions for certain genes against various genomes(for different organisms).
For example, I will blast regions 1..367, 368..444, 445..828 of the gene ACAN(https://www.ncbi.nlm.nih.gov/nuccore/NM_013227.3) against an organisms genome such as
ftp://ftp ...
written 2.4 years ago by
Jacob • 10
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