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.
29
questions
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12
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How to convert fasta file to tab delimited file
I have a fasta file like
>sample 1 gene 1
atgc
>sample 1 gene 2
atgc
>sample 2 gene 1
atgc
I want to get the following output, with one break between ...
- 965
191
votes
4
answers
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views
Why does the SARS-Cov2 coronavirus genome end in aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa (33 a's)?
The SARS-Cov2 coronavirus's genome was released, and is now available on Genbank. Looking at it...
...
- 1,725
22
votes
10
answers
7k
views
What is the fastest way to calculate the number of unknown nucleotides in FASTA / FASTQ files?
I used to work with publicly available genomic references, where basic statistics are usually available and if they are not, you have to compute them only once so there is no reason to worry about ...
- 5,632
19
votes
7
answers
17k
views
34
votes
4
answers
9k
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Why does the FASTA sequence for coronavirus look like DNA, not RNA?
I'm looking at a genome sequence for 2019-nCoV on NCBI. The FASTA sequence looks like this:
...
- 443
14
votes
10
answers
3k
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How to simulate NGS reads, controlling sequence coverage?
I have a FASTA file with 100+ sequences like this:
>Sequence1
GTGCCTATTGCTACTAAAA ...
>Sequence2
GCAATGCAAGGAAGTGATGGCGGAAATAGCGTTA
......
I also have a ...
- 2,739
3
votes
4
answers
484
views
How to programatically download SARS-CoV-2 fasta from NCBI/Genbank via API?
I would like to download a number of SARS-CoV-2 fastas from NCBI/Genbank using a web endpoint. I looked on their website but it's confusing.
I have the accession numbers, but can't figure out how to ...
- 409
0
votes
1
answer
2k
views
Using Entrez.efetch() to retrive .fasta file from any NCBI database?
I tried to use these python codes to retrieve a .fasta file from gene database, but the output were the parameters of the report
...
- 15
42
votes
4
answers
62k
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What is the difference between FASTA, FASTQ, and SAM file formats?
I'd like to learn the differences between 3 common formats such as FASTA, FASTQ and SAM. How they are different? Are there any benefits of using one over another?
Based on Wikipedia pages, I can't ...
- 1,323
28
votes
7
answers
10k
views
Read length distribution from FASTA file
I have a single ~10GB FASTA file generated from an Oxford Nanopore Technologies' MinION run, with >1M reads of mean length ~8Kb. How can I quickly and efficiently calculate the distribution of read ...
- 2,173
24
votes
4
answers
16k
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What Ensembl genome version should I use for alignments? (e.g. toplevel.fa vs. primary_assembly.fa)
When you look at all the genome files available from Ensembl. You are presented with a bunch of options. Which one is the best to use/download?
You have a combination of choices.
First part options:
...
- 1,603
13
votes
6
answers
411
views
Are there any databases of templates for common bioinformatic file formats?
I want some templates of different file formats that I can use to test my scripts and identify possible bugs in my code.
For example, consider nucleotide FASTA, a simple but often abused format, I ...
- 3,958
11
votes
3
answers
7k
views
Converting a VCF into a FASTA given a reference with Python, R
I am interested in converting a VCF file into a FASTA file given a reference sequence with Python or R.
Samtools/BCFtools (Heng Li) provides a Perl script ...
- 1,711
11
votes
1
answer
3k
views
Changing the record id in a FASTA file using BioPython
I have the following FASTA file, original.fasta:
>foo
GCTCACACATAGTTGATGCAGATGTTGAATTCACTATGAGGTGGGAGGATGTAGGGCCA
I need ...
- 496
9
votes
5
answers
4k
views
How can longest isoforms (per gene) be extracted from a FASTA file?
Is there a convenient way to extract the longest isoforms from a transcriptome fasta file? I had found some scripts on biostars but none are functional and I'm having difficulty getting them to work.
...
- 301
9
votes
10
answers
25k
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Remove/delete sequences by ID from multifasta
I have a fasta file like this:
>Id1
ATCCTT
>Id2
ATTTTCCC
>Id3
TTTCCCCAAAA
>Id4
CCCTTTAAA
I want to delete sequences that have the following IDs.
<...
- 385
8
votes
4
answers
1k
views
How to manipulate a reference FASTA or bam to include variants from a VCF?
I have some software which takes fastas as the input. I need to include SNVs and InDels from a VCF into the reference hg38 and then use this.
The problem is, I don't know of an algorithmically sound ...
- 1,711
5
votes
2
answers
899
views
How can I locate duplicated regions in a sequence?
I am facing an issue when trying to align short reads against a region in human chr5. The two Sensory Motor Neuron genes, (SMN1 and SMN2) are almost 100% identical and this causes the aligner to fail ...
- 10.5k
5
votes
4
answers
3k
views
How to map PDB chains to Uniprot IDs using API services
I have a lot of PDB IDs and I need to get uniprot fasta sequences of these PDB IDs special chains by API services. For example, imagine that I need to get fasta sequence of '1kf6' 'A' chain. The ...
- 777
5
votes
1
answer
905
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Ancestry of the coronavirus 2019-nCov, WuHan city, China
In one of the answers to another question about the corona virus a link was given to this phylogenetic analysis of the virus.
Can somebody assist a non-bio type here? It seems to show that the ...
- 153
5
votes
1
answer
184
views
Extracting sequences from FASTA beginning with common 5' end
I am trying to figure out the best way to extract sequences from a FASTA file which begin with a common 5' region of 43 nucleotides. Preferably, I would like to to allow for "fuzziness" in this region ...
- 53
3
votes
1
answer
133
views
How to use the hmmsearch on prototypic repetitive sequences Repbase Update database?
I want to use the hmmsearch proposed in Convergence of retrotransposons in
oomycetes and plants by Kirill Ustyantsev, Alexandr Blinov and Georgy Smyshlyaev. After the help from terdon I managed to ...
- 497
2
votes
1
answer
853
views
Remove Redundant Sequences from FASTA file in Python
I'm attempting to remove redundant sequences from a fasta file (from NCBI). When I execute this code, it returns the number of spots, not the number of sequences. (Number of spots: 408,293, Number of ...
- 53
2
votes
3
answers
4k
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Filtering Sequences (entries) by headers ID from a Fasta file database
First of all, sorry if this question has been posted previously (I could not found a solution accessing the previous Q&A).
I have a fasta file as follow:
...
- 21
2
votes
1
answer
410
views
How to edit the headers of multiple fasta files from multiple folders?
My directories are organized as follows: one main directory, in which I have multiple directories that end with a number ranging from 314 to 727, followed by .3 . For example, 'mgm4761314.3'. Within ...
- 1,017
2
votes
1
answer
1k
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remove sequences from fasta file matching a string in the header
I have a file with 16S sequences. some headers contain species information. For my purposes I would like to exclude a number of species from the file, therefore I would like to do a pattern matching ...
- 21
1
vote
2
answers
3k
views
Create BED file from list with gene symbols
Is there a way to generate a BED file of a list of gene symbols for a given genome?
- 345
1
vote
2
answers
245
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
votes
2
answers
59
views
How to obtain desired output?
I am working on a project using the following command within nano:
...
