All Questions
Tagged with phylogenetics fasta
66 questions
191
votes
4
answers
124k
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
34
votes
4
answers
9k
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:
...
- 443
12
votes
5
answers
25k
views
How to download FASTA sequences from NCBI using the terminal?
I have following accession numbers of the 10 chromosomes of Theobroma cacao genome.
...
- 361
7
votes
3
answers
154
views
How does one construct a cladogram of intraspecies relationships?
I have SNP data from several cultivars of rice which I have used to produce alignments, but I don't think that the usual models and algorithms used for generating phylogenetic trees are appropriate, ...
- 123
6
votes
4
answers
2k
views
multi-sequence alignment of samples with multiple contigs each
I want to perform a multi-sequence alignment on 12 samples that clustered based on cgMLST. Ultimate goal is to find out whether they differ by the presence of a few genes.
I have performed multi-...
- 283
6
votes
1
answer
136
views
Is there a way to assemble contigs starting from a specific sequence?
My work involves searching for marker genes/fragments in metagenomic databases (like the Sequence Read Archive). Once I find these sequences, I would like to know more about the neighboring genomic ...
- 1,027
5
votes
1
answer
905
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 ...
- 153
5
votes
3
answers
1k
views
How can I only get the species name for fasta sequences from blast results?
I am trying to make a phylogenetic tree from sequences obtained with blast. I have files that contains hundreds of fasta protein sequences which are all named like ...
- 51
4
votes
2
answers
487
views
How to align output of grep --color=always? (To QC fasta/fastq files)
Grepping out short sequences from a fasta or fastq file is a really useful way to look at sequencing data. Using the option --color=always makes this even more ...
- 3,201
4
votes
1
answer
239
views
Programmatic way of accessing the FASTA sequence similarity tool (or similar) in Python
I am looking for a tool that performs a sequence similarity algorithm for proteins. More specifically, I am looking for something that would be usable in Python (or anything else usable in the command ...
- 425
4
votes
1
answer
116
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 ...
- 41
3
votes
4
answers
1k
views
How can I add a ";" at the end of each fasta header line in a file?
I have a large fasta file with RNA sequences. I need to add a ; at the end of each header line (lines beginning with >) in ...
3
votes
4
answers
510
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
3
votes
2
answers
305
views
Understanding the fasta file format and using edit distance for alignment
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 ...
- 131
3
votes
2
answers
816
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: ...
- 3,201
3
votes
2
answers
425
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 ...
- 33
3
votes
1
answer
85
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 ...
- 377
3
votes
1
answer
71
views
compare fasta sequences in pairs and collect metrics
I have 96 fasta files (A1, A2, A3...) from one plasmid assembly pipeline, and I have another 96 fasta files (B1, B2, B3 ...) from another plasmid assembly pipeline.
I would like to compare pair ...
- 137
3
votes
2
answers
125
views
How can I resolve "missing name of population" message in PGDSpider?
I want to use Arlequin for AMOVA. I have my FASTA files which I want to convert into .arp files which are recognizable by arlequin. When I try to convert it using Population Genetics Data (format) ...
- 329
3
votes
2
answers
1k
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:
...
- 41
3
votes
3
answers
239
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 ...
- 31
3
votes
2
answers
229
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 ...
- 357
3
votes
1
answer
108
views
Downloading genes from NCBI in fasta format
I'm pretty new in bioinformatics.
I need to download FASTA sequences of several genes. The list of genes I have assembled consists of 140 genes, so I'd rather do this through via code than download ...
- 31
3
votes
1
answer
162
views
Compare and Reorganize Fasta Headers Python
I want to compare the headers from the fasta file to file1, and if there's a match, reorganize the header and put the match first. If there's no match between fasta file and file1, look at file2 and ...
- 33
2
votes
2
answers
1k
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 ...
2
votes
3
answers
390
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:
...
- 43
2
votes
2
answers
447
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,
...
- 109
2
votes
1
answer
47
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'...
- 409
2
votes
1
answer
118
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 ...
- 145
2
votes
2
answers
445
views
Elegant Way to Extract Gene Symbols from FASTA Headers
I've downloaded the RefSeq transcript sequences (FASTA format) for the GRC38 patch 14 build of the human genome and would now like to extract the gene symbols (only) in order from the headers. I'm ...
- 21
2
votes
1
answer
131
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 ...
- 128
2
votes
1
answer
71
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?
2
votes
3
answers
301
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 ...
- 191
2
votes
1
answer
249
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 ...
- 121
2
votes
0
answers
133
views
Phylogenetic tree from a large FASTA file
I want to create a phylogenetic tree using a 3.8MB FASTA file with ambiguous code. How can I perform multiple sequence alignment and the construction of phylogenetic tree with these ambiguous codes?
...
- 21
2
votes
1
answer
260
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 ...
- 79
1
vote
4
answers
663
views
Removing particular line along with Fasta header in fasta file
I have a fasta file of 3'UTR sequences of the genes. Some of the gene do not have a 3'UTR sequence and reported with sequence unavailable but there is FASTA header.
...
- 19
1
vote
3
answers
1k
views
How can I remove FASTA sequences with an asterisk inside the sequence?
I have several protein sequences with an asterisk in the middle of the sequence, and I'd like to remove those sequences.
In the example below, I have three sequences:
From this example, I would like ...
- 161
1
vote
3
answers
717
views
Edit all the fasta headers using awk
kindly your comment highly appreciated
have more than 4k header sequences look like:
...
- 386
1
vote
2
answers
97
views
How to know if FASTQ/BAM is from reference genome (FASTA)?
I'm new to bioinformatics. I have a problem in which I have a FASTA reference genome and lots of reads in FASTQ files. Some of them could be contaminants, so I'd like to filter them out and get only ...
- 151
1
vote
4
answers
1k
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 ...
- 1,423
1
vote
3
answers
3k
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 ...
- 123
1
vote
1
answer
162
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 ...
- 159
1
vote
1
answer
443
views
phangorn fasta file read error
Im trying to read a multifasta sequence file into phangorn I get the following error
...
- 1,854
1
vote
2
answers
76
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 ...
- 111
1
vote
1
answer
172
views
How to chop fasta / bed /peak file genomic segments into smaller fixed or custom genomic intervals
I am trying to split my .bed/.fa file genomic segments into arbitrary smaller overlapping intervals:
Consider a typical line/row in my *.bed file as follows:
chrom. $\ \ \ \ \ $ start $\ \ \ \ \ \ \ \...
- 343
1
vote
1
answer
150
views
Fixing FASTA file for Local BLAST Database
I recently prefetched 157 SRA files from an NCBI BioProject using the SRAtoolkit. I then used the toolkit to download those files in FASTA format.
Each individual FASTA file looks something like this:
...
- 1,063
1
vote
1
answer
194
views
Weird phylogenetic tree
I am required to create a phylogenetic tree(s) of my genes of interest and am currently blasting (tblastn) my genes of interest from S. mediterranea against model systems before expanding my search.
...
- 11
1
vote
2
answers
104
views
How to align two FASTAs and extract the aligned part?
I have two fastas and I'd like to align them to extract the aligned part. I've just found examples (Several of them) of alignment of FASTQs using FASTA references, so I'm not sure if what I want ...
- 151
1
vote
1
answer
179
views
Phylogeny building in R from FASTA files:
Im working on building a phylogeny from scratch with downloaded FASTA sequences from GeneBank. I think Im doing alright up until the multi sequence alignment in the ...
- 111