User: Hugo

gravatar for Hugo
Hugo290
Reputation:
290
Status:
Trusted
Location:
Universidade de Vigo, Ourense (Spain)
Website:
http://www.sing-group....
Last seen:
1 month, 2 weeks ago
Joined:
3 years, 3 months ago
Email:
h******@gmail.com

Posts by Hugo

<prev • 72 results • page 1 of 8 • next >
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Answer: A: SEDA (SEquence DAtaset builder): a desktop tool for processing FASTA files conta
... Dear community members, We have just released [SEDA 1.2.0][1], a new version of SEDA that includes three new operations and reduces the execution time of the *BLAST: two-way ortholog identification* operation. The new operations are: (i) *NCBI BLAST* and *UniProt BLAST* to run BLAST queries using t ...
written 11 weeks ago by Hugo290
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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 4 months ago by Hugo290
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Comment: C: FASTA file split
... Yes, it is GUI only. ...
written 5 months 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 5 months 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 6 months 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 6 months 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 6 months 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 6 months 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 6 months ago by Hugo290 • updated 6 months ago by RamRS30k
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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 7 months ago by Hugo290

Latest awards to Hugo

Scholar 7 months ago, created an answer that has been accepted. For A: Renaming FASTA headers while keeping some previous information?
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Renaming FASTA headers while keeping some previous information?
Scholar 7 months ago, created an answer that has been accepted. For A: Renaming FASTA headers while keeping some previous information?
Scholar 2.6 years ago, created an answer that has been accepted. For A: Renaming FASTA headers while keeping some previous information?
Scholar 2.8 years ago, created an answer that has been accepted. For C: Ballgown data reading problem
Teacher 2.8 years ago, created an answer with at least 3 up-votes. For A: Renaming FASTA headers while keeping some previous information?
Scholar 2.8 years ago, created an answer that has been accepted. For C: Ballgown data reading problem

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