User: Hugo

gravatar for Hugo
Hugo290
Reputation:
290
Status:
Trusted
Location:
Universidade de Vigo, Ourense (Spain)
Website:
http://www.sing-group....
Last seen:
4 hours ago
Joined:
2 years, 11 months ago
Email:
h******@gmail.com

Posts by Hugo

<prev • 71 results • page 1 of 8 • next >
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Answer: A: How do I remove certain sequences in fast based on header?
... You can try SEDA (https://www.sing-group.org/seda/). The *Pattern filtering* operation (https://www.sing-group.org/seda/manual/operations.html#pattern-filtering) would allow you to do this if you configure a *Not contains* pattern with the "^XR_" text. ...
written 15 days ago by Hugo290
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Comment: C: FASTA file split
... Yes, it is GUI only. ...
written 4 weeks ago by Hugo290
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Comment: C: FASTA file split
... Nice tutorial. We have developed **SEDA**, a tool for processing FASTA files, and it has two functions for file splitting: *Split* (https://www.sing-group.org/seda/manual/operations.html#split), and *Regular expression split* (https://www.sing-group.org/seda/manual/operations.html#regular-expression ...
written 4 weeks ago by Hugo290
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Comment: C: Filter Aminoacid sequences
... Not all users that need to deal with FASTA files can use the command line with confidence and efficiency enough to do their job. ...
written 10 weeks ago by Hugo290
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Answer: A: How to add file name after > in a multi-fasta file?
... You can use [**SEDA**][1], an open source application for processing FASTA files containing DNA and protein sequences. The *Rename header* operation has an *Add prefix/suffix* mode (https://www.sing-group.org/seda/manual/operations.html#add-prefix-suffix) that allows you to add the text you want at ...
written 10 weeks ago by Hugo290
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Answer: A: Filter Aminoacid sequences
... You can use [**SEDA**][1], an open source application for processing FASTA files containing DNA and protein sequences. The *Filtering* operation (https://www.sing-group.org/seda/manual/operations.html#id5) allows you to filter sequences using different criteria, including sequence length. [1]: h ...
written 10 weeks ago by Hugo290
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Comment: C: Parsing a portion of a fasta file header
... In case you can use a GUI-based software, I would recommend you to have a look at **SEDA** (https://www.sing-group.org/seda/), our open source application for processing FASTA files containing DNA and protein sequences. The online manual (https://www.sing-group.org/seda/manual/index.html) provides d ...
written 10 weeks ago by Hugo290
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Comment: C: Reading a tab separated file
... With `read.delim` you do not need to specify the separator as tabulator is used by default. Try this: dataset4 <- read.delim("./Documents/time_series/cbe.dat", colClasses = rep("numeric",3)) ...
written 11 weeks ago by Hugo290 • updated 11 weeks ago by RamRS27k
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Comment: C: Install BLAST in ubuntu
... You may also consider to use a Docker image for BLAST, like the ones available at the *pegi3s Bioinformatics Docker Images Project*: https://hub.docker.com/r/pegi3s/blast ...
written 11 weeks ago by Hugo290
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Answer: A: Remove stop codon containing sequences from multifasta(DNA) files
... Dear Shaminur, you can use **SEDA** ( https://www.sing-group.org/seda/ ). To do what you want, you should use the *Filtering operation* (https://www.sing-group.org/seda/manual/operations.html#id5) and check the option *'Remove sequences with in-frame stop codons'*. If you have any question, do not ...
written 11 weeks ago by Hugo290 • updated 20 days ago by geek_y11k

Latest awards to Hugo

Scholar 11 weeks ago, created an answer that has been accepted. For A: Renaming FASTA headers while keeping some previous information?
Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: Renaming FASTA headers while keeping some previous information?
Scholar 3 months ago, created an answer that has been accepted. For A: Renaming FASTA headers while keeping some previous information?
Scholar 2.2 years ago, created an answer that has been accepted. For A: Renaming FASTA headers while keeping some previous information?
Scholar 2.4 years ago, created an answer that has been accepted. For C: Ballgown data reading problem
Teacher 2.4 years ago, created an answer with at least 3 up-votes. For A: Renaming FASTA headers while keeping some previous information?
Scholar 2.5 years ago, created an answer that has been accepted. For C: Ballgown data reading problem

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