All Questions
Tagged with phylogenetics fasta
66 questions
1
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104
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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
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2
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97
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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
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1
answer
143
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How to remove third codon positions from a charset in iqtree?
I need to build a phylogenetic tree using IQ-TREE, starting from a sequence alignment in CODON format of several invertebrate mitochondrial genes. These are my charsets:
...
2
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0
answers
133
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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?
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- 21
3
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1
answer
71
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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
1
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1
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178
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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
3
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2
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125
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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
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1
answer
108
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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
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1
answer
162
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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
1
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4
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663
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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.
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- 19
1
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1
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113
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How to get full headers with tabs as separators with segmasker?
I try to pass a .fasta file with headers where tabs are used as separators as input file to NCBI BLAST+ segmasker:
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- 247
1
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1
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172
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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
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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
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3
answers
1k
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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
6
votes
4
answers
2k
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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
2
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2
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445
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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
1
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2
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102
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Generate consensus protein sequence from relatively gappy alignment?
I would like to know what would be the best way to generate a full-length consensus sequence?
I want to obtain a single representative sequence from a relatively gappy multiple sequence alignment of ...
- 2,364
3
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4
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1k
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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
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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
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
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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
0
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1
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233
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How to get a FASTA format file with the DNA sequences of all annotated genes?
I am analysing Pyrococcus Furiosus DNA sequencing data by considering data published here in NCBI. When I click on "Send to">"Gene Features">"FASTA format" I ...
0
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2
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404
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How to know if the DNA sequence has been assembled and why is it important to know how it was assembled?
I have downloaded my FASTA format files, that have the DNA sequences of the coding region of the genes and the DNA sequence of the complete genome, from NCBI. How can I recognize if these sequences ...
2
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2
answers
1k
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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
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
0
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1
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2k
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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
3
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2
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425
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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
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0
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48
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Combine two alleles to genotype locus?
I have a following fasta (produced by stacks populations):
...
- 11
-1
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1
answer
183
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Does anyone know how I can convert DNA code into FASTA for this TTGAAACACTGGATGAATGAAAAGCCCTGCTTTGCAACCCCTCAGC [closed]
TTGAAACACTGGATGAATGAAAAGCCCTGCTTTGCAACCCCTCAGC this is the DNA code Sequence. I have tried converting each into the amino acid and ended up with this LKHWMNEKPCFATPQX but I was told that this isn't ...
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3
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3k
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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
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2
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59
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How to obtain desired output?
I am working on a project using the following command within nano:
...
0
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2
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147
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How to fix NameError?
I am working on a project and am having issues with the following code that I have written in nano:
...
1
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1
answer
162
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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
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0
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40
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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 ...
- 15
1
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1
answer
47
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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 ...
- 121
3
votes
2
answers
305
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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
1
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1
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443
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phangorn fasta file read error
Im trying to read a multifasta sequence file into phangorn I get the following error
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- 1,854
1
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2
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76
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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
0
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1
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61
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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 ...
- 317
2
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1
answer
131
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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
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1
answer
71
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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?
1
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4
answers
1k
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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
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3
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717
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Edit all the fasta headers using awk
kindly your comment highly appreciated
have more than 4k header sequences look like:
...
- 386
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
5
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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
191
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4
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124k
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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
0
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1
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26
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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:
...
- 359
2
votes
1
answer
118
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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
12
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5
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25k
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How to download FASTA sequences from NCBI using the terminal?
I have following accession numbers of the 10 chromosomes of Theobroma cacao genome.
...
- 361
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3
answers
301
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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