User: tlawrence3

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tlawrence360
Reputation:
60
Status:
New User
Location:
United States
Last seen:
3 years, 8 months ago
Joined:
3 years, 10 months ago
Email:
t*********@ucmerced.edu

Posts by tlawrence3

<prev • 10 results • page 1 of 1 • next >
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Answer: A: Searching all proteins for a short degenerate consensus sequence
... You can do this easily by installing the FAST: Fast Analysis of Sequences Toolbox (publication)(github). You can install it by using this command (only use sudo if you need to): (sudo) perl -MCPAN -e 'install FAST' You will also need the fasta files containing human and mouse proteins. You can g ...
written 3.8 years ago by tlawrence360
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Comment: C: Searching all proteins for a short degenerate consensus sequence
... What is the degenerate amino acid sequence? ...
written 3.8 years ago by tlawrence360
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Comment: C: Extract fasta sequences from a large file using a list of names
... It is not a bug. fastA format is loosely defined as: >identifier<space>description<newline> <sequence data> So when you don't have a space in the header line all you have is an identifier which fasgrep searches by default. So instead of: fasgrep -di which searches the des ...
written 3.9 years ago by tlawrence360
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Comment: C: Extract fasta sequences from a large file using a list of names
... I guess my bash scripting skills need some improvement. Since I am one of the authors of the toolkit I want to make sure it is working for as many people as possible. ...
written 3.9 years ago by tlawrence360
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Answer: A: What is the effect of Best_hit_overhang and Best_hit_score_edge on number of sub
... -qcov_hsp_perc does exactly what you think it does. However, it says it takes a float so if you want 100% coverage I would try both and see which gives the desired results: -qcov_hsp_perc 1.0 -qcov_hsp_perc 100 ...
written 3.9 years ago by tlawrence360
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Comment: C: Extract fasta sequences from a large file using a list of names
... What didn't work? Did you get an empty fasta file? The wrong sequences? An error? Does doing the command manually give the expected results? ...
written 3.9 years ago by tlawrence360
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Comment: C: Extract fasta sequences from a large file using a list of names
... I updated the script. It should work now.   ...
written 3.9 years ago by tlawrence360
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Comment: C: Extract fasta sequences from a large file using a list of names
... It is something in the bash script. I don't know bash scripting well enough to figure it out. This works on the command line: fasgrep -di "Paenibacilus borealis" fasta_file.fa However, it doesn't work in the script. Maybe someone here can help. ...
written 3.9 years ago by tlawrence360
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Comment: C: Extract fasta sequences from a large file using a list of names
... Updated the example to make it more clear. ...
written 3.9 years ago by tlawrence360
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Answer: A: Extract fasta sequences from a large file using a list of names
... You can do this easily by installing the FAST: Fast Analysis of Sequences Toolbox (publication)(github). You can install it by using this command (only use sudo if you need to): (sudo) perl -MCPAN -e 'install FAST' Once it is installed here is a small bash script to do what you need: #!/bin/ba ...
written 3.9 years ago by tlawrence360

Latest awards to tlawrence3

Scholar 3.8 years ago, created an answer that has been accepted. For A: Extract fasta sequences from a large file using a list of names
Teacher 3.9 years ago, created an answer with at least 3 up-votes. For A: Extract fasta sequences from a large file using a list of names
Scholar 3.9 years ago, created an answer that has been accepted. For A: Extract fasta sequences from a large file using a list of names

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