Questions tagged [fasta]
To be used for questions specific tothe sequence file format `.fasta`. Please minimise usage if the question is more generally about sequence formats.
17
questions with no upvoted or accepted answers
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Phylogenetic tree from a large FASTA file
I want to create a phylogenetic tree using a 3.8MB FASTA file with ambiguous code. How can I perform multiple sequence alignment and the construction of phylogenetic tree with these ambiguous codes?
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- 21
2
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60
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Why do I obtain different output results with blast vs awk commands
I have an awk command that identifies 30 pb from two multifasta files.
When I used two input files:
E.g. 100 sequences each, I get the same result with the ...
- 41
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133
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How to extract Genbank sequence and identify ORFs from the sequence in R?
I used
ape::read.GenBank
and then used the function
ORFik::findORFs
to find ORFs in the sequence of interest. But the former ...
- 430
2
votes
1
answer
240
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Merging ssu-align alignments
ssu-align is an HMM-based MSA tool for ribosome's small subunit (SSU) sequences. It's bundled with three SSU models:
archaeal,
bacterial
eukaryotic
Approach Given a set of archaeal and ...
- 79
1
vote
1
answer
108
views
Remove files after process is terminated
In my pipeline nextflow, I create a channel with channel.fromSRA and the channel contains lots of heavy files.fastq.gz. Then I have a first process to unzip files and transform them in files.fasta and ...
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53
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How can I get the HGVS notation of a mutation from a FASTA?
In an old article, they gave a table of mutations found in a gene and its positions which points to another article containing the FASTA sequence.
This FASTA is the precursor sequence of the gene. How ...
- 1,105
1
vote
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answers
296
views
How to calculate distance matrix from fasta?
I’d like to perform the following, but I am having difficulty.
I want to convert amino acid sequences in multifasta files into matrices (or vectors) with Euclidean distance and Pearson correlation ...
- 11
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15
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Can FASTA data be submitted directly into eCTD submission to the FDA?
We are getting sequence data from microbiota samples as part of a FDA submission identifying changes in Micobiota from skin samples over time and compared with different treatments. the data will be ...
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119
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How can I extract sequences from FASTA file using OTUs ID?
I have one FASTA file with sequences and headers, and one OTUs table.
What I want to do is replace the current headers in the FASTA file with just the OTU IDs from the .txt file. The files look like ...
- 41
1
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27
views
How can I speed up FASTA ssearch output?
I'm trying to predict targets for miRNA sequences, and so far after reading some papers for other tools that do this, I've found that I should be using FASTA's ...
- 111
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41
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Combine two alleles to genotype locus?
I have a following fasta (produced by stacks populations):
...
- 11
1
vote
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88
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Is there a FASTA Sequence Description Nomenclature to Indicate a Split Sequence or Subsequence?
I have a nucleotide sequence where I am interested in aligning reads distinctly to one or another portion of the sequence. However, I would like to use a visualization tool such as IGV to view these ...
- 36
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44
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I have two files: mys.nuc and ms.prep and need to use bioseq to extract the ORF sequences and save as “mys.nuc2”
Below are the two files I am working with:
...
- 63
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22
views
adding multiple files in folder and zipping in loop
Through fasterq-dump, I am generating 2 files in 1 run of loop. I want to club these two files (A_1.fastq & A_2.fastq) in one folder and zip the it.
...
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40
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What tool(s) can I use to use a .faa file to feed into JSMol?
JSMol, the molecular modelling software, requires PDB file format to work and render the graphics. Currently, I am writing an annotation software - backend in Perl - that takes in a .faa file (fasta ...
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84
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Extracting and analyzing structure data of multiple proteins from PDB using Python
I am new to programming and I am given the task to extract structural data of soluble proteins from PDB and then shortlist the soluble enzymes from the extracted data set for further classification ...
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39
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Please help me with my command!
I am looking for a command to count the total number of unique proteins in a file. For instance I wrote a command to BLAST XYZ proteins as query against the DLY proteins as a database to determine the ...
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