Questions tagged [fasta]

should be used for questions specific to sequence file format `.fasta`. should **not** be used if you just used fasta file, or if the question is more general about sequence formats.

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21 views

How do I get repeating regions from fasta file or directly from internet

If I go to ncbi site, apply customize view -> Customize -> All features -> Update view and then ctrl + f : Alu I can ...
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2answers
39 views

Python: How to write duplicate sequences removed from fasta file to new file

I currently am using this code to remove duplicate sequences from the fasta file. However, I would also like to write a new file with only the removed duplicates as well as a count for how many times ...
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1answer
57 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 ...
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20 views

How to compare 2 AGTC sequences of homo sapiens and pan troglodytes?

I'm the beginner and I want to compare DNA of Homo sapiens and Pan troglodytes. I have taken files from here and downloaded homo sapiens primary assemmly file and pan troglodytes toplevel file, but ...
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58 views

What is the full script to extract sequences from fasta file by using Ids in text file in python 3 and pycharm?

I have a fasta file (gene.fasta)with sequences with names patterns: ...
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20 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 ...
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79 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 ...
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4answers
359 views

Edit FASTA header using sed

I need to rename the following headers from a FASTA file. Something like: ...
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1answer
50 views

How can i modify FASTA headers in a multi fasta file using BioPython SeqIO

I have a multi fasta file similar to this (relatively new here so uncertain of best way to present this; I have gone for an output and the code i used to make it - belt and braces...): ...
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4answers
62 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 ...
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1answer
75 views

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 ...
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1answer
25 views

After completing the evaluation, how to predict PTM lysine or any other modification with unlabeled data for making a web server?

I have created a model with SVM classifier and evaluated it with 5-fold cross-validation. The dataset was sequence data containing lysine modified sites. Now I want to build a web server where anyone ...
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2answers
60 views

Is it possible to go from a digital sequence to an actual nucleotide?

I'm trying to learn about what the state of technology is at presently. It seems like we clearly can go from nucleotide to digitally stored sequence, but can we transcribe something from the digital ...
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1answer
20 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:...
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1answer
41 views

Relationship between the instantaneous rate of change of a continuous time Markov model and the rate of a global clock model?

If continuous-time Markov models contain a parameter q that denotes the instantaneous rate of change and a global/strict clock model is the overall rate of evolution, how are these two parameters ...
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22 views

How to find the region with frequent mutation?

I am very new to bioinformatics and I was wondering if I can get some help regarding finding region that has high mutation rate. Currently, I have 2 fasta files, one that is aligned and one regular ...
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1answer
26 views

Cutting the sequence into several sequences with the information of a dataframe

I have a fasta file with several 120-concatenation protein sequences. I also have a data frame with 120 names of proteins in column 1 and their length in column 2. Using this dataframe I want to ...
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1answer
32 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 ...
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1answer
41 views

Identifying proteins in a concatenated protein sequences [closed]

I have a 120-concatenated protein sequence in a fasta file. I would like to split by proteins. How can I identify each protein?
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3answers
49 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 ...
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14 views

Retrieve FASTA sequences using sequence ids in cdbfasta

I'm using cdbfasta command to retrieve sequences using ids, all works well but I find some sequences repeated in my output and the command does not retrieve all the sequences I want.
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3answers
105 views

Edit all the fasta headers using awk

kindly your comment highly appreciated have more than 4k header sequences look like: ...
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5answers
8k views

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: ...
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1answer
1k views

Is it possible for coronavirus or SARS to be synthetic?

I have heard several conspiracy theories regarding the origin of the new coronavirus, 2019-nCov. For example that the virus and/or SARS were produced in a laboratory or were some variant of Middle ...
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250 views

Using BaseRecalibrator in GATK4

GATK4's BaseRecalibrator uses a list of known variants to adjust the base quality scores in a BAM file. I would like to visualize the pre and post recalibration ...
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2answers
787 views

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 ...
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4answers
84k 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... ...
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1answer
78 views

Interpreting MultiQC plot of GATK BaseRecalibration data?

I'm using GATK4 to build a somatic variant calling pipeline. The pipeline uses MultiQC to aggregate quality control data, and one of the QC measures reported is base quality score recalibration from ...
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4answers
200 views

Convert FASTA to FASTQ with dummy quality scores

I have a FASTA file which I would like to convert into FASTQ format as the tool I want to use my data in requires it in FASTQ format. So dummy quality scores are fine. Note: I am not using any ...
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1answer
89 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: ...
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0answers
18 views

Obtaining HGDP project data in fasta format

I need to obtain sample data from modern humans in fasta format. I just need some megabytes of data from every individual. I actually use a script that obtains the cram file from here (ftp.1000genomes....
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1answer
19 views

SRA Toolkit and lebanese data

I am trying to extract data from this: https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR6245218 I installed SRA Toolkit, downloaded the SRR6245218 file and executed this: ...
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1answer
49 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 ...
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1answer
35 views

Bedtools get fasta and ORF from a blastX run

Hello I made a blastX research (A query genome in nucleotide format translated into protein in 6 reading frames against a protein dabatase) And here is a head of ...
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5answers
2k views

How to download FASTA sequences from NCBI using the terminal?

I have following accession numbers of the 10 chromosomes of Theobroma cacao genome. ...
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0answers
43 views

Extract secondary structures and sequences from dssp files

I have a very messy problem and I really need your help. I have a lot of dssp files in a folder. Every dssp file contains informations about proteins. Also, I have a separate file containing two ...
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3answers
122 views

16S species-level taxonomic assignment--what is the current state of the art?

We currently use DADA2 for picking ASVs and the assignTaxonomy funciton for assingment to genera. Google does bring up various recent articles on species-level ...
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1answer
239 views

Filtering fasta files by ID

I have this code to filter some IDs from a fasta file: ...
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1answer
89 views

How to edit the headers of multiple fasta files from multiple folders? (recursively)

This is an expansion of my previous question, 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 ...
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1answer
67 views

Weird phylogenetic tree

I am new to research. As part of my MRes, I am required to create a phylogenetic tree(s) of my genes of interest. I am currently blasting (tblastn) my genes of interest from S. mediterranea against ...
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1answer
97 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 ...
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1answer
113 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)
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2answers
88 views

MiXCR: only create a single export file for all clonotypes

I am using following command from MiXCR to both align, assemble and export my input files: ...
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2answers
320 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: ...
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1answer
251 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: ...
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1answer
75 views

Are there any resources for calculating / representing evolutionary relationships within gene clusters?

I am working with a gene cluster found in several species. The genes involved are pretty much the same, with the odd insertion, but they can be often found in different orientations. So, I can't just ...
3
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1answer
60 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
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1answer
221 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 ...
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0answers
25 views

return cds from a protein fasta based on gene ID in unix?

I'm trying to retrieve cds sequences for given genes. Which requires taking a list of genes gene27 gene28 Retrieving their Gene ID (LOC##) and using faa to ...
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1answer
65 views

Subset a protein fasta based on sequence length?

I have a strange protein fasta file. There are several entries for the same gene and I need to extract the entry with the longest width. ...