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.

15 questions with no upvoted or accepted answers
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1answer
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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 ...
3
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1answer
40 views

Counting hexamers in fasta sequence and identify its structure (and interruptions)

I have a lot of fasta files, each one with thousand of reads containing the hexameric motif "CCCTCT". The hexameric motif is highly continuous in most cases but interruptions may occur. I ...
2
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0answers
45 views

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 ...
2
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0answers
97 views

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 ...
1
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0answers
54 views

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 ...
1
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0answers
20 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 ...
1
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0answers
32 views

Combine two alleles to genotype locus?

I have a following fasta (produced by stacks populations): ...
1
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5answers
171 views

How to remove duplicates from a fasta file using python

I am using the following command: ...
1
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0answers
86 views

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 ...
1
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0answers
42 views

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: ...
0
votes
2answers
80 views

Concatenate multiple fasta files into one file for MLST

I have seven fasta files, one per gene, with more than 400 fasta entries per file, like this: Input: Gene1.fasta ...
0
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1answer
143 views

Converting Fastq files to Fasta files on Ubuntu

I am new to bioinformatics and programming. I tried to convert my fastq files to fasta file, but got this. What could be wrong? ...
0
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1answer
69 views

Metagenome simulation from a concatenated FASTA file

I am trying to simulate metagenome sequencing. So I will start with a file with a lot of concatenated genomes. From there, I would like to randomly extract 10,000 sequences of length 200bps. I got ...
0
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0answers
52 views

Python/Biopython - Replace amino acid residue on MSA with "z" from a list of unaligned positions

I'm trying to programmatically replace a set of amino acid residues on an MSA with a "Z" from a list of unaligned positions. Any ideas on how I could do this? Input: a list of unaligned ...
0
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0answers
37 views

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 ...