Questions tagged [sequence-analysis]

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merging two/or more bed file into one bed file

I am trying to merge two bed files (more in future) to one. my bed files are something like : . I need to merge them in a way to have the shared chromosome location. Is there a way to do that ?
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Understanding some of the computational bottlenecks of Covid-19 research

I am a researcher in high-performance computing (with very little bioinformatics background), and I am trying to understand what are the current biggest computational bottlenecks of softwares used for ...
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Coding object structure properties into a sequence

Hopefully, I found the right place to ask. Please, note that I'm not a specialist in the current field. Is there an algorithm to code information about object structural properties into a sequence (...
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35 views

Overlap in Paired-end Reads for Sequencing?

Regarding Sequencing: Do/can the paired-end reads have overlaps?
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Location of Reads in Sequencing

I have questions regarding sequencing: Are paired-end reads from different stands? What about single reads, are they coming from both strands?
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28 views

Warning in fastqc

I am checking the quality control of my sequences using the Fastqc tool. For some steps, like "Per base GC content", etc., I received a warning. So, I was wondering whether I Should also take care of ...
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38 views

SRA run data access

Trying to download run data of Run accession SRR2155174. Here's the link: https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR2155174 Please go to the link and go to the "Data Access" tab. Hereunder ...
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1answer
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NCBI SRA database sample: control vs test

I was trying to download some data from NCBI SRA (SRA059451). There are 27 samples available for SRA059451. But i am unable to understand which samples are 'control' and 'test' samples. Please help me ...
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Tools or softwares for clustering evaluation

I am using a few clustering algorithms as well as my own tool for protein sequences. Also, I have benchmarked clustering results (i.e. ground truth) to compare with the results. Is there any tool/...
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1answer
27 views

Download sequences of isoforms

I want to collect all isoforms of all genes (Fasta/Fastq file of nucleotide and protein sequences) Arabidopsis Col-0. I am wondering if there is a straightforward way to download the file from any ...
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21 views

What kind of error-correction code is used in the error-correction code DNA sequencing?

In 2017, Chen et al reported a DNA sequencing technology called error-correction code (ECC) sequencing [1]. They borrowed ideas from communication and coding theory and encoded information redundency ...
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1answer
87 views

Any user friendly way to find rare mutations in whole genome raw?

Is there any user friendly way to find rare mutations in the individual human whole genome sequencing raw data? (from Dante, 30x coverage). To be more specific, I want to find mutations from this ...
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1answer
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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 ...
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working with cutadapt

I'm working with ion torrent data where I apply the program cutadapt. I'm analyzing ITS seq data, as well as Matk. When I'm using cutadapt, I search the information for this genes, and built new ...
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1answer
79 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)
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75 views

How to reproduce this specific sequence logo from 10 000 human mRNAs?

this is A sequence logo showing the most conserved bases around the initiation codon from 10000 human mRNAs. I would like to reproduce this sequence logo. How can I get the sequences? which database ...
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1answer
59 views

Is there a convention or standard of the highest bits in a sequence logo? [duplicate]

In bioinformatics, a sequence logo is a graphical representation of the sequence conservation of nucleotides (in a strand of DNA/RNA) or amino acids (in protein sequences). wiki says The total ...
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1answer
314 views

How to compute the Shannon entropy for a strand of DNA?

I'm confused by the computation of sequence logo. Wikipedia gives a process about this without a concrete example. Let's just consider DNA, so there are 4 bases (nucleic acids). The following data ...
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1answer
101 views

Why do ten rows (Figure_1) correspond to 2 bits (Figure_2) in a sequence logo?

Following this question, I'm confused with the computation of sequence logo Following data comes from the book "Machine Learning - A Probabilistic Perspective (Figure_1)" here is the corresponding ...
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1answer
180 views

What is “aligned sequences” and “consensus sequence” in the context of sequence logo? How to compute these?

In bioinformatics, a sequence logo is a graphical representation of the sequence conservation of nucleotides (in a strand of DNA/RNA) or amino acids (in protein sequences). so, What is "aligned ...
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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 ...
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How to use extractfeat?

I am working on a script on bash linux to get the CDS (coding sequence) of a gene using extractfeat by EMBOSS. It gives me the error: Warning: No sequences written to output file I am unsure if my ...
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3answers
209 views

Deep learning RNA sequences

Currently I'm working on a project, which combines deep learning with RNA sequences. I'll try to predict pseudotorsion angles [1] from raw rna sequence. The ideas is to train a neural network with raw ...
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1answer
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Generating DNA sequences with constraints

I would like some advice on potential strategies to address the following problem. I want to write a program that will generate DNA sequences that are optimized on two constraints based on an input ...
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1answer
133 views

Protein SCA and DCA

Could you please suggest suitable R packages for statistical coupling and direct coupling analysis of protein sequences? I know there are Python packages for those: SCA and DCA. I was looking for ...
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3answers
374 views

CDS length for each human gene

Does anyone know where and how could I download a list of all human genes and the length of the coding sequence for each gene? Is it possible to do this on the NCBI site, ensembl?
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Building cancer gene database

I am trying to build a database of different cancer genes i.e lung cancer, throat cancer etc. Searched through NCBI website by searching for nucleotide sequences, but I am unable to find appropriate ...
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1answer
882 views

What is a quick way to find the reverse complement in bash

I have a DNA sequence of which I would like to quickly find the reverse complement. Is there a quick way of doing this on the bash command line using only GNU tools?
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1answer
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Genome annotation of a Bacillus strain

I finished the sequencing of the genome of a biocontrol activity strain Bacillus amyloliquefaciens by Illumina hiseq. I have already gone through some papers but there were no details of processing in ...
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1answer
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How to allow “half windows” in biopython?

I am using Biopython to examine protein sequences including the Kyte and Doolittle hydrophobicity. However, for short sequences, this returns an empty value; the value is not allowed if the window ...
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How to find the position-specific weight matrix (PSWM) for a list of genes having different sizes?

Wiki has the algorithm for finding position-specific weight matrix (PSWM) for a list of nucleotide sequences having an equal number of nucleotide. How do we find the PSSM for a list of nucleotide ...
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1answer
37 views

Download program for ΔG for TM insertion

I am trying to calculate the ΔG of TM insertion for many protein sequences. Has anyone come across the source code or a programmatic version for the von Heijne ΔG for TM insertion? The web server is ...
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2answers
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Retrieve RNA sequencing data for human p53 colon cancer cell lines

I want to download the next generation RNA sequencing data in different cell lines. I want the data (alongwith normal) for p53 wild type, p53 knock-out and p53 null cell lines (human colon cancer). ...
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2answers
1k views

Hardware Requirements (specs) for Bioinformatics-dedicated desktop [closed]

I know this is a somewhat general or vague question, but I’m interested in your opinions. I must build a desktop for general bioinformatics activities with human genomes. I will work with Python and R ...
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1answer
45 views

De novo motif discovery in protein sequences

I am trying to build a features matrix to be used for Random Forest based classification. I'd like to add, as features, short motifs which are common to all the protein sequences belonging to a ...
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Sequencing Deciduous Plants

Firstly, I'm personally not in the field of Bioinformatics, so apologies if this is a dumb question. Does anyone know of any research that has been carried out on the sequencing of deciduous plant ...
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Codon usage analysis for whole genomes

I am new to bioinformatics. So if these questions seem you to a bit childish please forgive me. I have two queries. I am intending to perform a codon usage analysis followed by correspondence ...
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1answer
133 views

Tool to show DNA sequence and allowing upload of own graph data

Background We want to be able to load (or request) data for a genome including the sequence and gene annotation (bacteria). Then, we want to load our own annotation which should be displayed as a ...
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1answer
187 views

Fastqc- Per Base Sequence Quality

I am trying to figure out how to interpret the "Per Base Sequence Quality"? What does Position in reads (bp) mean? Also in order to draw this box-plot graphics, more than one quality scores are needed ...
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2answers
530 views

Python API for working with ENSEMBL genomes

Dear bioinformaticians, I could find two python APIs to mine ENSEMBL genome databases. There is a pyensembl which is more popular and then there is ...
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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 ...
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1answer
1k views

Better aligner than bowtie2?

Bowtie2 is probably the most widely used aligner because of it's speed. Burrow-wheeler (BW) algorithms (including bwa) tend to ...
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Finding parameters to separate 2 genes

If I have dataset of genetic sequences of 2 genes performing different things: how can I separate them? I want to find underlying differences between the 2 classes and common things among the 2 ...
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1answer
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Is there any tools that can generating FBA model from genome sequences or proteome sequences?

Suppose I have all sequences of genes or proteins of certain species, are there any free tools I can use to generate a flux balance analysis model out of them? What I was thinking is more like to ...
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2answers
1k views

What is cellranger doing in comparison to other methods?

I've recently started working with the 10X-Genomics platform with Illumina (MiSeq and HiSeq) for single-cell RNA-Seq. I've been recommended the "cellranger" (version 2.1.0) which I understand handles ...
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1answer
102 views

How to predict the distance between two residues in a protein sequence

I have some protein sequences and I need to predict the physical distance between each two residues in the protein when folded correctly in 3 dimensions; I need to predict this distances just by ...
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1answer
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SNP data Download Help

I am new to the field of Bioinformatics. Single Nucleotide Polymorphism or SNP data are available on the the Internet to download.SNP related data are valuable for variety of reasons ranging from ...
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1answer
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Error while Importing fastq sequences to jMHC software

I am trying to analyze my .fastq files (MiSeq exon reads) with the jMHC software, but output files I have obtained have no results. I think I might be doing something wrong during the first step: "...
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2answers
202 views

Books on bioinformatics algorithms

I'm looking for a book about bioinformatics algorithms, such as alignment, BLAST search, and variant calling. I'm hoping reading about this subject will give me a deeper understanding of the ...
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1answer
363 views

Combine Fastq by writeFastq is not working properly

Currently I have 4 fastq file for each patient as WES data. For WES pipeline, I want to combine those fastq files. I am using writeFastq from ShortRead package in Bioconductor.But I think this ...