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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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 ...
D.J.'s user avatar
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1 answer
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Dealing with X Residues in FASTA files prior to folding analysis

We are working with a large dataset of proteins for folding/docking tests across various tools (AlphaFold, ESM2, RoseTTAFold). In some of the FASTA files, there is an X for a non-standard residue. An ...
Brian Root's user avatar
1 vote
4 answers
310 views

Remove sequences from a fasta file with IDs from a text file using Python

a python beginner here. I have a fasta file with 2500+ sequences, and after doing some analysis I want to remove around 200+ sequences based on the matching IDs. Now, I have one fasta file (as sample....
Irfan's user avatar
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1 vote
1 answer
98 views

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: ...
Francesco De Giglio's user avatar
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What is the troubleshoot for this error: conversion of .SRA to FASTA file on command prompt?

I am getting this error message after using the following code: C:\sratoolkit.3.0.7-win64\sratoolkit.3.0.7-win64\bin>fastq-dump --fasta SRR1658345 Error: ...
Sanjukta Ghosh's user avatar
1 vote
1 answer
53 views

Get a certain gene sequence from bam/vcf and reference

I need to get a fasta sequence of a certain gene for a certain worm strain that is different from reference. I have a reference genome, BAM for the strain of interest, and coordinates of the gene. I ...
user98747's user avatar
2 votes
0 answers
19 views

How to identify TF binding motifs?

I have DNA sequences from a single gecko species for a set of genes (SULF1, SOX9, SAL1), I wanted to compare the putative promoter sequences for each gene, and compare them to the promoter regions of ...
JohnDoe23's user avatar
1 vote
2 answers
115 views

Making a DNAStringSet object

I wish to download a fasta sequence from NCBI using "rentrez" package and then save it in an object, then I want to have this object as a DNAStringSet object to work on the sequence using &...
Farzad Beikpour's user avatar
3 votes
1 answer
168 views

How to analyze GC content of fasta file?

I have the assembly file of a certain lizard species, I wanted to recreate Fig. 2 of the following paper, which compares the GC content distribution over 5kb windows, how would I go about doing this? ...
JohnDoe23's user avatar
-1 votes
1 answer
64 views

stats.sh error in BBmap package

I am trying to calculate the N50 value from the assembled FASTA file. I used stats.sh from the BBmap package. I executed the following command ...
seq's user avatar
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4 votes
2 answers
313 views

Keeping DNA sequence after changing FASTA header on command line

I have a FASTA header that looks like this: ...
rimo's user avatar
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0 answers
25 views

adding multiple files in folder and zipping in loop

Through fasterq-dump, I am generating 2 files in 1 run of loop. I want to club these two files (A_1.fastq & A_2.fastq) in one folder and zip the it. ...
Shradha Sharma's user avatar
1 vote
1 answer
47 views

how to search and calculate occurence of certain word (like TAA) in fastafile

...
tonu's user avatar
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2 votes
0 answers
121 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? ...
user17615's user avatar
3 votes
1 answer
64 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 ...
cautree's user avatar
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1 vote
2 answers
89 views

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 ...
rimo's user avatar
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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 ...
Harish Prabhakar's user avatar
1 vote
1 answer
145 views

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 ...
Rajag's user avatar
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3 votes
2 answers
75 views

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 ...
irritable_phd_syndrome's user avatar
1 vote
1 answer
90 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 ...
I Del Toro's user avatar
1 vote
1 answer
155 views

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 ...
eva fonta's user avatar
0 votes
2 answers
302 views

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 ...
Amal's user avatar
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3 votes
3 answers
2k views

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 ...
Supertech's user avatar
  • 596
1 vote
4 answers
190 views

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 ...
rimo's user avatar
  • 963
5 votes
4 answers
488 views

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&...
rimo's user avatar
  • 963
2 votes
1 answer
674 views

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%) ...
pubsurfted's user avatar
3 votes
2 answers
107 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) ...
Nickmofoe's user avatar
  • 339
1 vote
1 answer
837 views

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 ...
Jackson Xavier's user avatar
1 vote
1 answer
480 views

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 ...
Shafayet Rahat's user avatar
1 vote
4 answers
144 views

Grep peculiar pattern inside a file

I would like to grep everything inside the second square bracket of a file: ...
Marco's user avatar
  • 161
3 votes
1 answer
72 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 ...
Vjon's user avatar
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1 vote
1 answer
181 views

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 ...
thole's user avatar
  • 143
3 votes
1 answer
152 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 ...
nora job's user avatar
1 vote
4 answers
556 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. ...
Dr Sud's user avatar
  • 19
3 votes
1 answer
363 views

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: ...
rimo's user avatar
  • 963
0 votes
2 answers
171 views

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 ...
Santosh's user avatar
1 vote
1 answer
99 views

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: ...
maciejwww's user avatar
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1 vote
0 answers
61 views

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 ...
user324810's user avatar
  • 1,115
1 vote
1 answer
128 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 $\ \ \ \ \ \ \ \...
Zebra Fish's user avatar
1 vote
1 answer
120 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: ...
rimo's user avatar
  • 963
2 votes
3 answers
844 views

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 ...
Amit's user avatar
  • 133
1 vote
0 answers
329 views

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 ...
Farinelli's user avatar
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 ...
Marco's user avatar
  • 161
1 vote
0 answers
17 views

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 ...
John McLane's user avatar
1 vote
1 answer
346 views

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 ...
Sowmya Pulapet's user avatar
6 votes
4 answers
903 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-...
BCArg's user avatar
  • 283
1 vote
2 answers
354 views

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 ...
Sam's user avatar
  • 19
2 votes
2 answers
343 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 ...
Mark Pauley's user avatar
3 votes
3 answers
1k views

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 ...
Cornelius Roemer's user avatar
2 votes
2 answers
230 views

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 (...
Cornelius Roemer's user avatar

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