Questions tagged [fasta]

should be used for questions specific to sequence file format `.fasta`. should **not** be used if you just used fasta file, or if the question is more general about sequence formats.

Filter by
Sorted by
Tagged with
0
votes
1answer
19 views

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: ...
2
votes
1answer
22 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 ...
1
vote
1answer
17 views

Bedtools get fasta and ORF from a blastX run

Hello I made a blastX research (A query genome in nucleotide format translated into protein in 6 reading frames against a protein dabatase) And here is a head of ...
3
votes
4answers
140 views

How to download FASTA sequences from NCBI using the terminal?

I have following accession numbers of the 10 chromosomes of Theobroma cacao genome. ...
0
votes
0answers
20 views

Extract secondary structures and sequences from dssp files

I have a very messy problem and I really need your help. I have a lot of dssp files in a folder. Every dssp file contains informations about proteins. Also, I have a separate file containing two ...
1
vote
1answer
62 views

Filtering fasta files by ID

I have this code to filter some IDs from a fasta file: ...
0
votes
1answer
78 views

How to edit the headers of multiple fasta files from multiple folders? (recursively)

This is an expansion of my previous question, How to edit the headers of multiple fasta files from multiple folders? My directories are organized as follows: one main directory, in which I have ...
2
votes
1answer
41 views

How to edit the headers of multiple fasta files from multiple folders?

My directories are organized as follows: one main directory, in which I have multiple directories that end with a number ranging from 314 to 727, followed by .3 . For example, 'mgm4761314.3'. Within ...
2
votes
1answer
43 views

How to convert VCF format file into Fasta(.fa) with the Reference data

I need a Software or Python Program for Converting VCF(.vcf) to FASTA(.fa) format with the help of reference (.fa)
0
votes
2answers
44 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: ...
3
votes
2answers
104 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: ...
2
votes
1answer
44 views

Concatenate multiple fasta files into one file per unique entry

I have eight fasta files, one per gene, with 106 fasta entries per file, like this: gene1.fasta: ...
3
votes
1answer
127 views

How can I locate duplicated regions in a sequence?

I am facing an issue when trying to align short reads against a region in human chr5. The two Sensory Motor Neuron genes, (SMN1 and SMN2) are almost 100% identical and this causes the aligner to fail ...
0
votes
0answers
18 views

return cds from a protein fasta based on gene ID in unix?

I'm trying to retrieve cds sequences for given genes. Which requires taking a list of genes gene27 gene28 Retrieving their Gene ID (LOC##) and using faa to ...
0
votes
1answer
62 views

Subset a protein fasta based on sequence length?

I have a strange protein fasta file. There are several entries for the same gene and I need to extract the entry with the longest width. ...
2
votes
1answer
40 views

how to merge two fasta based on full fasta header and remove the duplicate

I am wondering if anyone can help to merge two fasta file based on the full header as initially gene ID may be similar in some of the sequences and to remove the duplicate entry based on full fasta ...
0
votes
1answer
40 views

Function to find ATP binding sites

I'm currently doing a python project where I need to write code that extracts the ATP binding site from a FASTA file using a regular expression. I've tried the following code but it does not work. It ...
3
votes
2answers
135 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, ...
2
votes
3answers
254 views

How to reverse complement the DNA sequences for given inverse/reverse coordinates?

I have the series of coordinates in id.txt file, whose coordinates sequences are in genome.fasta file. The coordinates of id.txt ...
0
votes
0answers
52 views

Reconstructing reference FASTA from CRAM file

I would like to reconstruct (or download) the original FASTA reference file that was used to create a CRAM file in my possession. I realize that I can download the contigs specified in the CRAM header ...
2
votes
1answer
52 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 ...
5
votes
1answer
75 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 ...
0
votes
2answers
74 views

Downloading Fasta for each chromosome of a complete genome

Whatever I am googling I am not able to find fasta file of each chromosome for hs37d5.fa. hs37d5.fa whole fasta file however is here ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/technical/reference/...
4
votes
1answer
651 views

Splitting fasta file into smaller files based on header pattern

I have to split this fasta files into smaller files and write them into individual files my files ...
3
votes
3answers
142 views

GTF from consensus sequence

I am new to using bioinformatic tools and I was hoping this community could help clear something up for me. I need to generate a gtf file. My data are a set of complete HA genes for influenza B ...
1
vote
2answers
40 views

Get & Annotation of isomiR (isoform of miRNA) profile from RNA-seq

I should get and analyse isomiR (isoform of miRNA) profile from RNA-seq with FASTA format. The best tool for this is "DeAnnIso". But here is a problem with this tool, it only allows you to upload ...
2
votes
4answers
933 views

Can a gff file be converted to a fasta file?

I downloaded an annotated genome file in gff format here. I would like to use it for proteomics. Though I need it in fasta format. Is there any tool that converts gff to annotated fasta? I see the ...
6
votes
2answers
287 views

How do I re-name the headers of my Fasta file?

I appologize for asking this, but I really am really bad with regex... Can someone help me transform the headers of my fasta files from this: ...
3
votes
1answer
328 views

scRNA-seq, 10x cellranger pipelines

I'm starting to do sc-rnaseq using 10x cellranger pipelines, and i add TdTomato sequence to mouse reference genome and add an entry in the gtf. My code is But when I makref, it remindered that: ...
5
votes
1answer
106 views

How to find all variable-length seqs with an exact 5' and 3' match in a FASTA file

Context I am interested in finding all of the promotors specific to a particular sigma factor. I have identified the -35 and -10 sites from the literature, bold denotes -10, -35, binding sites: <...
2
votes
1answer
109 views

Question about research in bioinformatics for Computer Science student [closed]

I am a computer science student, who was interested in taking research in the field of bioinformatics. The first research idea I had was to make a model that could predict the possibility of type 2 ...
2
votes
5answers
988 views

How to create a .bed file from .fasta? [duplicate]

I have some problems with creating a .bed file for hg19 which I will be able to load on IGV. The fasta file contains rows of this form: ...
4
votes
2answers
115 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 ...
1
vote
2answers
93 views

convert tRNA coordinates Result to Fasta format

I believe many of the experts here have gone through this issue, I have run tRNAscan-SE on my genome to predict all the tRNAs, and have successfully gotten all the tRNA coordinates like start, end ...
5
votes
3answers
500 views

finding unique headers in a fasta file using linux command line

I tried to use the following command uniq -u reference.fasta >> reference_uniq.fasta I'd like a count of the unique headers.
5
votes
1answer
84 views

Extracting sequences from FASTA beginning with common 5' end

I am trying to figure out the best way to extract sequences from a FASTA file which begin with a common 5' region of 43 nucleotides. Preferably, I would like to to allow for "fuzziness" in this region ...
2
votes
0answers
49 views

How to extract Genbank sequence and identify ORFs from the sequence in R?

I have extracted the sequence using the function ape::read.GenBank and found the function ORFik::findORFs to find ORFs in the ...
6
votes
4answers
445 views

Convert SRA to FastA

I'm trying to get the FastA files for some accessions (like NC_001416.1). I did not managed to find an FTP server or direct link to these files (I want to get it from command line with ...
2
votes
2answers
75 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
votes
4answers
255 views

How to merge transcript sequence with same name in a FASTA file.

Suppose we have a fasta file like ...
3
votes
2answers
94 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 ...
2
votes
1answer
334 views

How to concatenate FASTAs with respect to chromosome?

I have the following two small FASTAs, dna1.fa and dna2.fa: ...
5
votes
3answers
1k views

How do I rename fasta headers?

I am trying to use the seqkit replace command to replace chromosome names in the format chr_I, chr_II, ... to I, II, .... I am ...
2
votes
1answer
55 views

HIVdb program and FASTA sequence input

I am trying to use HIVdb(https://hivdb.stanford.edu/hivdb/by-sequences/) program. I have a HIV protease which I want to test with most commonly used PIs. But when I entered it in fasta sequence format ...
3
votes
1answer
405 views

How to extract the protein fasta file from a genbank file?

Let's say I have a genbank file, e.g. the one downloaded from here, that contains entries as ...
4
votes
1answer
175 views

Finding proteins in a sequence

I have a file with protein sequences, all on a single line, like this: ...
1
vote
1answer
348 views

I need to use my code with fasta format. Can anybody help?

I need some help. I have written a program that simulates protein cleavage but I need to modify it so that it produces fasta formatted output. here is all of my sequence in .fas file ...
3
votes
5answers
5k views

Remove/delete sequences by ID from multifasta

I have a fasta file like this: >Id1 ATCCTT >Id2 ATTTTCCC >Id3 TTTCCCCAAAA >Id4 CCCTTTAAA I want to delete sequences that have the following IDs. <...
6
votes
1answer
147 views

Run gffread in multi-thread mode

Is there any possibility to run gffread in multi-thread mode? The answer seems to be 'no' from the manual (or gffread -h), as no multi-thread option is mentioned. ...
5
votes
1answer
210 views

Can a data file in VCF format be converted into FASTA?

I'm considering purchasing the 'MyGenome' product by Veritas Genetics to analyze my genome for a project. I'd like the data to be in FASTA format, but Veritas only provides VCF data. Is it possible to ...