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.

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4
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1answer
242 views

Finding proteins in a sequence

I have a file with protein sequences, all on a single line, like this: ...
4
votes
1answer
301 views

Counting a specific consecutive character with its occurrence position and length

I have a sequence file and want to count consecutive character "N", with the tandem's position of occurrence and its length. Say I have a file named mySequence.fasta...
3
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5answers
4k views

How to create a .bed file from .fasta? [duplicate]

I have some problems in creating a .bed file for hg19, so I will be able to visualize the .bed file in IGV. The .fasta file contains rows of this form: ...
3
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4answers
4k views

Can a gff file be converted to a fasta file?

I downloaded an annotated genome file in gff format here. I would like to use it for proteomics. Though I need it in fasta format. Is there any tool that converts gff to annotated fasta? I see the ...
3
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4answers
629 views

How to merge transcript sequence with same name in a FASTA file.

Suppose we have a fasta file like ...
3
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1answer
2k views

How to extract the protein fasta file from a genbank file?

Let's say I have a genbank file, e.g. the one downloaded from here, that contains entries as ...
3
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3answers
274 views

GTF from consensus sequence

I am new to using bioinformatic tools and I was hoping this community could help clear something up for me. I need to generate a gtf file. My data are a set of complete HA genes for influenza B ...
3
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2answers
156 views

How to map reads shorter than 32bp with minimap2?

I mapped fasta sequences to a reference. The fasta sequences range in length from 17bp up to several hundred bp. I used minimap2 with the following command: ...
3
votes
2answers
179 views

How to find/build the evolutionary history of a protein from its sequence?

I'd like to build the evolutionary history of a protein, given its sequence. Namely, given a FASTA entry how can I build an evolutionary tree? Here is the 5wxy protein as an example: ...
3
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3answers
452 views

sort a fasta file containing the Oxford Nanopore Technologies (ONT) header by sequencing start_time ascending

I have basecalled ONT reads and converted them to multifasta. The multifasta contains the original ONT headers in this format: ...
3
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1answer
72 views

For phylogenetic tree construction from core-genome which one is preferable: amino-acid based MSA or nucleotide based MSA?

The genomes are from same species. Is it true that, in phylogenetic tree constructed from amino-acid based MSA (multiple sequence alignment) some information are lost, so for phylogenetic ...
3
votes
1answer
312 views

How to generate two fasta files from samtools phase output?

samtools phase is an easy-to-use tool to phase variants from a bam file and a reference. For a sequence that has two haplotypes, like this: ...
3
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2answers
667 views

How to find common sequences among 6 multi-fasta files

I have 6 multi-fasta files, every of them contains ca 1500 sequences like that: ...
3
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3answers
177 views

Effect of mutation in DNA sequence on transcription factor binding sites

How much does a single mutation/alteration of a nucleotide affect the presence of a transcription factor binding site (TFBS)? I am from computer science background(Obviously). I want to make a ...
3
votes
2answers
109 views

Is there a tool that can take a protein's amino acid sequence and would display it's locus on the genome?

I have the UNIPROT IDs, PDB IDs and FASTA files of several known proteins. I am looking for a tool that can take as input the protein's amino acid sequence and display the coding nucleotides of those ...
3
votes
1answer
551 views

scRNA-seq, 10x cellranger pipelines

I'm starting to do sc-rnaseq using 10x cellranger pipelines, and i add TdTomato sequence to mouse reference genome and add an entry in the gtf. My code is But when I makref, it remindered that: ...
3
votes
1answer
131 views

Question about research in bioinformatics for Computer Science student [closed]

I am a computer science student, who was interested in taking research in the field of bioinformatics. The first research idea I had was to make a model that could predict the possibility of type 2 ...
3
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1answer
95 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 ...
3
votes
1answer
1k views

SPAdes error during assembly

I try to perform a hybrid assembly using Unicycler. Unicycler use SPAdes to assembly the illumina sequences, and the program crashes while in SPAdes. The spades.log file says something about an ...
3
votes
1answer
47 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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3answers
299 views

How to extract subset of protein structure (PDB format) file based on a subsequence of that protein

I looking at a particular protein structure called 2LY4 accessible from RSCB PDB website. The corresponding fasta sequence for that structure is this: ...
2
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4answers
100 views

Separate multiple sequence into different file, one sequence per file

I have a file contain multiple sequence, and I want to separate them by "gene:" into different file. example: example.fa ...
2
votes
1answer
1k views

Concatenate multiple fasta files into one file per unique entry

I have eight fasta files, one per gene, with 106 fasta entries per file, like this: gene1.fasta: ...
2
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2answers
116 views

Sequence allignment with suffix array?

I'm writing the code from scratch and not using libraries for the actual indexing/search since it's a project for school. Any blackbox advice is fairly useless. I'm planning on aligning some short ...
2
votes
2answers
179 views

Understanding the fasta File Format

I'm a computer scientist teaching algorithms development in the Fall. One of the algorithms we teach is called Edit Distance, and our folklore is that it is used to compare RNA sequences (is this ...
2
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3answers
831 views

How to reverse complement the DNA sequences for given inverse/reverse coordinates?

I have the series of coordinates in id.txt file, whose coordinates sequences are in genome.fasta file. The coordinates of id.txt ...
2
votes
1answer
323 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 ...
2
votes
2answers
286 views

Issue with visualising cladogram/phylogenetic tree with multiple sequence alignment data in R?

I would like to visualize tree with multiple sequence alignment. My din.newick file is shown below, ...
2
votes
1answer
172 views

Does Prokka or gff3 change the sequence / subject ID of fasta files?

I used prokka to create a database for some fasta files but I noticed a strange difference between the prokka and fasta files. Normally the seqid for the gff3 output for prokka has seqid's that match ...
2
votes
1answer
509 views

Converting aligned fasta to plink ped/bed

I have an alignment of multiple sequences in a FASTA file (output from MAFFT), for which I would like to simulate a phenotype using plink, but for that I need to have my alignment in a PED file or ...
2
votes
1answer
34 views

Phasing problem using "samtools phase"

so I'm having a problem using samtools phase. I'm trying to phase my .bam archives that where generated by aligning my samples with my reference genome. Following the documentation I tried the command:...
2
votes
1answer
67 views

How to extract hypervariable region of mitochondrial dna from its fasta file?

Recently I've done some analysis on human mitochondrial DNA and now I want to run the same analysis on only hypervariable regions of mitochondrial DNA to see whether the changes that I have observed ...
2
votes
1answer
584 views

How to convert VCF format file into Fasta(.fa) with the Reference data

I need a Software or Python Program for Converting VCF(.vcf) to FASTA(.fa) format with the help of reference (.fa)
2
votes
1answer
177 views

how to merge two fasta based on full fasta header and remove the duplicate

I am wondering if anyone can help to merge two fasta file based on the full header as initially gene ID may be similar in some of the sequences and to remove the duplicate entry based on full fasta ...
2
votes
1answer
598 views

How to concatenate FASTAs with respect to chromosome?

I have the following two small FASTAs, dna1.fa and dna2.fa: ...
2
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1answer
28 views

Python package or CLI tool outputting mutations of sequence with respect to reference

I'm new to bioinformatics, and I'm looking for a tool that takes two FASTA files, one containing a reference, let's call it A.fasta, the other another sequence, let'...
2
votes
1answer
90 views

How to construct the phylogenetic tree of the "High Recombination" genus streptomyces?

I need to construct the phylogenetic tree of the whole genus of streptomyces. And my goal is to find out how my target strep species distributed in the whole strep genus and obtain the distribution ...
2
votes
1answer
90 views

Alignment for predicting DNA hybridization?

I am currently working on a Computer Science project where we are trying to build a large set of orthogonal single-stranded DNA sequences. The goal would be to ensure that when put in solution, the ...
2
votes
1answer
63 views

HIVdb program and FASTA sequence input

I am trying to use HIVdb(https://hivdb.stanford.edu/hivdb/by-sequences/) program. I have a HIV protease which I want to test with most commonly used PIs. But when I entered it in fasta sequence format ...
2
votes
0answers
46 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
votes
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 ...
2
votes
1answer
184 views

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 ...
1
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4answers
2k views

Edit FASTA header using sed

I need to rename the following headers from a FASTA file. Something like: ...
1
vote
2answers
86 views

How to identify the DNA sequence of a gene in the complete genome sequence FASTA format file?

I need to identify the sequence of a gene in the complete genome sequence . I thought it was simple, instead it is not a straightforward task ! My method was the following: I downloaded the FASTA ...
1
vote
3answers
415 views

Edit all the fasta headers using awk

kindly your comment highly appreciated have more than 4k header sequences look like: ...
1
vote
1answer
881 views

Filtering fasta files by ID

I have this code to filter some IDs from a fasta file: ...
1
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2answers
99 views

Can the header line contain arbitrary text in FASTA format?

The following is a valid .fasta file content: ...
1
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4answers
92 views

Tools for comparing/visualizing FASTAs?

I have two FASTAs/assemblies of the same species, but the bases are somewhat different. I would like to explore this. What tools/methods exist to compare two FASTAs and see the difference in ...
1
vote
1answer
438 views

I need to use my code with fasta format. Can anybody help?

I need some help. I have written a program that simulates protein cleavage but I need to modify it so that it produces fasta formatted output. here is all of my sequence in .fas file ...
1
vote
1answer
63 views

How do you replace multiple sequence names with new names using python?

I have into a dictionary some sequences. I would like to replace the sequences name for new names contained into a dataframe. ...