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.
226
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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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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 ...
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54
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Combine separate fasta files from a list.txt
I have about 10 fasta files that I need to pull from a giant folder of other fasta files (has about 100 files). I have a list of the files I need in a .txt file separated by line and I want to pull ...
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What tool(s) can I use to use a .faa file to feed into JSMol?
JSMol, the molecular modelling software, requires PDB file format to work and render the graphics. Currently, I am writing an annotation software - backend in Perl - that takes in a .faa file (fasta ...
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58
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How to align multiple contigs? To generate full length genome
I have MAG geneome sequence released in NCBI. In the released sequence there are 4915 contigs present. I want to get the full length genome sequence as FASTA file to proceed with further works like ...
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57
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Which candida albicans fasta and gff file should I use for alignment?
I downloaded the gff and fasta files for candida albicans from http://www.candidagenome.org. I want to use hisat2 to align some fastq files against it.
There are ...
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54
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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 ...
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79
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Remove files after process is terminated
In my pipeline nextflow, I create a channel with channel.fromSRA and the channel contains lots of heavy files.fastq.gz. Then I have a first process to unzip files and transform them in files.fasta and ...
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137
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open and read Fasta file (raw data)
I have a big fasta.dataset file containing half a million proteins (1.0 GB). I have four lines for each protein code:
line 1:the protein code
line 2: protein ...
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616
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How to write FASTA records using "Bio.SeqIO.write()"
Update:
Biopython document says that "Bio.SeqIO.FastaIO.FastaWriter" class is obsolete. Now my question becomes how to I use Bio.SeqIO.write() fucntion to ...
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155
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How to remove empty files from a directory?
I have a directory of FASTA files, some of which are empty (placeholders that were output from a pipeline) and I would like to delete the empty files using a for loop on the command line.
From what I ...
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445
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How to rename a file based on a directory name?
I have a lot of FASTA files that I recently scaffolded with RagTag. The output of RagTag includes a directory for each sample and the corresponding FASTA file written as "ragtag.scaffold.fasta&...
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438
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How to manually trim FASTA file sequences with the information provided in the header and store it into a new FASTA file? - Python
I have a FASTA file that has reads like this:
>SRR5655563.745 745 length=126 (type=T,start=2,end=12,length=11,identity=81.8182%) ...
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89
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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) ...
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296
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Need to convert .bed to .vcf. Can the reference build (and necessary .fasta) be determined for a .bed file?
I have some .bed files (and .bim and .fam files) containing data for a number of different samples, and I need to convert them to .vcf.
I've found bed2vcf which is ...
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194
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split fast reference fast file by 22 chromosome
HG38 human reference is the collection of reference from all 22 chromosomes,x,y chromosomes, and some others. I was targeting to split the reference file into 22 chromosomes fasta files. I am ...
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144
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Grep peculiar pattern inside a file
I would like to grep everything inside the second square bracket of a file:
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59
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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 ...
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78
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finding matching motifs in a sequence and their position
I am trying to find some matching motifs on a sequence, as well as the position that the motif is located in and then output that into a fasta file. The code below shows that the motif ...
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145
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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 ...
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363
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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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206
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Using SED command in Nextflow script
I was wondering if someone can help me figure out this error message. I’m at the end of my Nextflow pipeline and I want to change the header in a FASTA file and it works when I use this command:
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99
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How to find restriction enzyme frequency in whole genome and count the distance between them?
I am having possibly a simple question which is proving difficult.
My objective is to take the reference FASTA file and flat file database with 1500 restriction enzymes with its cutting sites (mostly ...
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82
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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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How can I get the HGVS notation of a mutation from a FASTA?
In an old article, they gave a table of mutations found in a gene and its positions which points to another article containing the FASTA sequence.
This FASTA is the precursor sequence of the gene. How ...
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66
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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 $\ \ \ \ \ \ \ \...
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65
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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:
...
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501
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change/edit FASTA headers
I have a FASTA file with 97,000 entires arranged like this :
>tr|A0A075B6G3|A0A075B6G3_HUMAN Dystrophin OS=Homo sapiens OX=9606 GN=DMD PE=1 SV=1
I want to have ...
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241
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How to calculate distance matrix from fasta?
I’d like to perform the following, but I am having difficulty.
I want to convert amino acid sequences in multifasta files into matrices (or vectors) with Euclidean distance and Pearson correlation ...
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648
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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 ...
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Can FASTA data be submitted directly into eCTD submission to the FDA?
We are getting sequence data from microbiota samples as part of a FDA submission identifying changes in Micobiota from skin samples over time and compared with different treatments. the data will be ...
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209
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Different line length in fasta file
I am currently using VEP for variant annotation.
I am facing an error as below:
[E::fai_build_core] Different line length in sequence 'Pn9'
I understand there is ...
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4
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427
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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-...
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Converting .bw files to .fq (fastq)
I am able to convert .bw files to .fq(fastq) manually in Shell, but I would like to automate the process coz I have hundreds of .bw file that I need to convert. Till now, I could think of following ...
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267
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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 ...
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How to get strain names/ids contained in a multi FASTA file using seqkit?
FASTA files can be very big and unwieldy, especially if lines are at most 80 characters, one can't speed up browsing them by using less with ...
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Checking that two multiline FASTAs are identical (allowing for different order and lower/upper case)
Is there a good CLI tool that can diff two multiline fasta files, ignoring order, and comparing sequences with identical names with each other pairwise.
Bonus points if lower/upper case is tolerated (...
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63
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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 ...
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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 DNA sequences. I need to add a ; at the end of each header line (lines beginning with >) in ...
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254
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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 ...
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207
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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 ...
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Displaying BIC and AICs from MSA nucleotide multisequence fasta file
I am initiating a project reproducing MEGA style trees using R to find the best DNA protein models under AIC/BIC. I have read the R AICs and BIC documentation but I'm struggling to implement this.
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317
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makeblastdb creating multiple files of unexpectedly large sizes
I have a set of 100 amino acid sequences and I want to perform a BLASTP sesrch against the refseq_protein database. Accordingly I had set up the standalone version ...
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81
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Extracting and analyzing structure data of multiple proteins from PDB using Python
I am new to programming and I am given the task to extract structural data of soluble proteins from PDB and then shortlist the soluble enzymes from the extracted data set for further classification ...
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142
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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.
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82
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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 ...
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I have two fasta files READ1 and READ 2. How to identify which one is the reverse and the forward?
As you can see in the picture I have two files from the paired end reads. I would assume READ1 would be forward reads and READ2 would be reverse reads, but my lab colleague told me that that might not ...
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838
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Concatenate multiple fasta files into one file for MLST
I have seven fasta files, one per gene, with more than 400 fasta entries per file, like this:
Input:
Gene1.fasta
...
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76
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How to plot the gap distribution of contigs wrt to reference genome
I have a contigs file that I generated using Minia and then I have used Minimap2 to map these contigs again to the reference genome. Now I want to plot the gap distribution i.e. gap distance of the ...
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Transfer annotations from one genome assembly to another
I've got an annotated draft genome assembly made using short and long read strategies. I've also done optical mapping to stitch some of the contigs together, with the goal being chromsome-length ...
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