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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22 views

How to get matching pattern along with ID in a single command in grep?

I have a file containing multiple fast sequneces. For a specific consensus pattern as input, I extracted all the matching patterns from target fasta sequences with ...
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1answer
53 views

How to write multi-sequence alignment data frame as a fasta format fast

I have a data frame where the row names are the species names, and each column can either be an Amino-Acid character or "-". I wish to write it in a fasta format. Simple example of the ...
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40 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 ...
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1answer
75 views

Biopython SeqIO check input file

Hi I am trying to learnt python3 and Biopython, I am trying to check imported fasta file before processing so far using: ...
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1answer
54 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 ...
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1answer
30 views

Metagenomics: Identifying most common sequences

I am working on a project and used the following command: ...
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3answers
107 views

Convert a fasta file to Newick format

My problem is (should be) pretty simple. I have a series of 10 sequences which I wish to convert into a Newick format file - what would be good software to do this? I've tried using Jalview and am ...
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2answers
20 views

FASTA and PDB: How to specify chain?

For proteins that have multiple chains (e.g., 1EMS), is there an easy way to specify which chain I want to use for blastp? I cannot imagine that I am the first person to have this problem, but so far ...
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2answers
64 views

How to replace sequence identifiers in a fasta with OTU IDs from another file?

I'm pretty new to Unix and bioinformatics and having a hard time accomplishing the following. I have one FASTA file with sequences and headers, and one OTU ID mapping file (.txt) with OTU IDs and ...
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1answer
62 views

How to remove duplicates from a fasta file using python

I am using the following command: ...
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2answers
39 views

How to obtain desired output?

I am working on a project using the following command within nano: ...
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2answers
47 views

How to fix NameError?

I am working on a project and am having issues with the following code that I have written in nano: ...
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1answer
20 views

Convert sequence in MS doc to fasta or genbank

How can I convert a sequence provided in a Microsoft doc file into a fasta or genbank format?
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1answer
41 views

Is there a simple command for outputting a tab delimited columns?

I am working on a fasta file and am writing my command in nano within command-line and executing using python, also within a command line. My objective is to get my command to provide me with a tab ...
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2answers
31 views

Extract sequences from MultiFASTA aligned file, by coordinates

I am trying to extract a specific sequence from a multifasta file, from each sequence in the aligned file. The sequences look like this, and there are 32 sequences within the multiFASTA: ...
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1answer
61 views

How to find the number of contigs produced? N50 length in base pairs? N90 length in base pairs?

I am having trouble with some underlying questions about my project. I have ran a Trinity tool to create a trinity.fasta file. To determine some underlying questions, I used the utility asm_stats to ...
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1answer
42 views

Get raw genome sequence

I'm currently working on testing some matching algorithms for strings. I would like to do some tests on raw genomic data as I expect different results from random strings given the lower entropy. How ...
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1answer
19 views

How to identify to each scaffold a read belongs to, inside a .sam file?

I have a fasta file assembly and combining it with the raw reads we produced a .bam file which I converted to .sam . The .sam information lines look like this: ...
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38 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 ...
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36 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 ...
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1answer
37 views

How to identify unknow bacterium species from whole genome genetic sequence

I am a Biochemist that is unfamiliar with bioinformatic tools and new to academia as a whole. I am currently using ILLUMINA PE data, which I trimmed (Trimmomatic), corrected (Rcorrector) and assembled ...
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1answer
30 views

Add segregating sites to branches of a tree

I'm trying to figure out how I would plot a tree with number of segregating sites on display on the branches I'm using acctran from phangorn to plot a parsimony tree (using phydat object from fasta ...
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2answers
55 views

get sequences begining with TA [closed]

I have a fasta file and the sequences in them are arranged like this: ...
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0answers
28 views

Why do I get cytosine to guanine/adenine transitions in bisulphite treated sequences?

I got my sequencing results (bisulphite treated and non treated sequences of same species Allium cepa) and now I have to do analysis in Cymate online tool. I prepared all sequences as it is written in ...
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3answers
54 views

Get gene sequence based on the annotation

I've got the reference genome with Python like so: ...
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2answers
152 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 ...
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1answer
66 views

Split fasta file based on groups in header information and output as separate files

I have a fasta file containing the sequence of a gene across different species. In total there are around 900 samples and 12 species. (Each sequences is over multiple lines and longer than 100bp.) My ...
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2answers
44 views

Basic question about finding mRNA sequence in transcriptome

I am a computer scientist just starting out in bioinformatics topics, and would appreciate any guidance that can be given here: I have an mRNA sequence- an isoform - whose length is about 4000 base ...
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1answer
21 views

Calculating Isoelectric point from a multifasta file

I need to calculate Isoelectric point from a multifasta file, is there any python code or web tool that allows me to do that?
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1answer
38 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
83 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
115 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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23 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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1answer
540 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: ...
2
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1answer
163 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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0answers
85 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
969 views

Edit FASTA header using sed

I need to rename the following headers from a FASTA file. Something like: ...
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1answer
72 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
71 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
297 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
26 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
62 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 ...
2
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1answer
24 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
52 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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0answers
24 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 ...
2
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1answer
40 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
43 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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4answers
65 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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0answers
15 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.