Questions tagged [sequence-alignment]

Use this tag to refer to the alignment of nucleotide or peptide sequences, producing an arrangement that maximizes similarity between sequences.

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

How to find adapter sequence

I have this GSE dataset ( GSE104279 ) (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE104279) I want to run cutadapt, but how would I find the adapter sequence so I can run cutadapt?
0
votes
1answer
45 views

Get list of urls of GSM data set of a GSE set

I have this GSE dataset ( GSE104279 ) (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE104279). I want to make a table with set IDs and ftp urls to use it as a table in galaxy.org I know that we ...
1
vote
0answers
26 views

Fastq dataset after clustering

I'm doing a project for DNA archival storage systems Is there an open-source dataset used as ground truth for clustering? E.g A file containing the ground truth strand sequences, which have been ...
0
votes
0answers
36 views

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 ...
2
votes
2answers
106 views

Filtering out reads from a reference (e.g. rRNA) using bowtie2

As I understand it, bowtie2 can easily be used to split reads into one of two groups: reads for which both of a pair align well to a reference (using e.g. ...
1
vote
0answers
28 views

Filtering pileup from site lists

I want to write a script that filters a pileup file from a site lists file. As an input I get a reference genome, pileup and site lists files. Example of an output for this script: Pileup File : ...
1
vote
1answer
54 views

How does sequence alignment help with protein folding prediction? [closed]

I've been seeing using sequence alignment to help with prediction of protein folding, but am unable to understand why. Google returns other research papers for these search terms, hence I'm hoping the ...
0
votes
0answers
20 views

Blast templates not found in PSI-TM Coffee

I'm trying to run psicoffe mode on Ubuntu 18.04, but it returns the error: 17633 -- WARNING: Impossible to find BLAST Templates Check that your blast server is properly installed [See documentation][...
0
votes
0answers
77 views

workaround for error: Bad CPU type in executable c

I use clustal() from library ape every now and then, but now it doesnt work... code: sylvia.clus = clustal(sylvia.seq) Error: ...
0
votes
1answer
22 views

Installation of PRANK MSA in WLS Ubuntu 20.04 LTS

I want to install PRANK on the Windows 10 Linux subsystem (Ubuntu 20.04 LTS), I have followed the installation instructions to no avail. ...
1
vote
1answer
58 views

How to understand methylation level?

For Bisulfite Sequencing data, we can calculate methylation level for a specific locus, $$ \mbox{methylation level} = \frac{\mbox{# methelyated reads}}{\mbox{# total reads}} $$ Here I think, for this ...
1
vote
0answers
24 views

What are the symbols of $*$ and '$\_$' in an unknown alignment format for HLA data from the IMGT dataset?

Has anyone worked with the IMGT HLA database/dataset before? IMGT-HLA git repo they have some convenient text files (eg. link to gene A .txt file) with the genomic data for the different alleles of ...
2
votes
1answer
49 views

mBED has time complexity $O(n \lg n)$, claimed by Clustal Omega paper, why?

In the Clustal Omega paper, it says the following about mBED ($N$ is the number of input sequences, I assume): we use a modified version of mBed (Blackshields et al , 2010), which has complexity of $...
0
votes
1answer
34 views

Display a score or graph to visualize the degree of conservation of each residue from alignment data

I would like to display a score or graph to visualize the degree of conservation of each residue from the amino acid alignment data. If possible, I'd like to extract the parts of the game that scored ...
1
vote
1answer
37 views

DiffBind, diffferentially binding site

I have data for 3 histone marks (2 for silencing and 1 for activation) each mark has three replicates. when I run the diffBind package I have three contrast: ...
1
vote
1answer
62 views

Comparing aligned amino acids to codon

I have a set of 4 amino acids which i have aligned,but i want to compare then with respective nucleotide sequence in terms of change codon level. I have the alignment file where i want to take only ...
0
votes
0answers
96 views

Calculate Entropy for DNA Multiple Sequence Alignment in R

I am pretty new to R. So I apologize for asking maybe a very basic question. Let's say I have a fasta file with sequence below: ...
1
vote
1answer
78 views

Do you know a program/script to count how many sequences have mismatches on each position of my primers?

I'm working with primer analysis and design, and so far I've performing it in Excel but: a) I don't like Excel, b) I do it manually, c) I don't like Excel, d) it gets tedious when working with ...
0
votes
1answer
235 views

Can't align 2 sequences, (MAFFT killed)

I have 2 .fa sequenes like: ...
0
votes
1answer
22 views

Non-exome variants called from whole-exome sequencing data

I'm working on rather standard whole-exome sequencing data and treat it the same as whole-genome sequencing data (aligning it to the full GRCh38 reference assembly and calling variants with no exome-...
0
votes
0answers
38 views

BLAST, last step: Needleman-Wunsch + S-score

In my bioinformatics course we studied the BLAST agorithm. After finding the HSP's and joining the HSPs together that are close enough and in a correct diagonal trend, we perform a next step: namely a ...
-1
votes
1answer
65 views

Compare nucleotide mutation with amino acid

To begin with I have two nucleotide sequence to compare I want to see how they might have evolved in terms of sequence similarity and differences. One of the way i can think of is align the sequences. ...
3
votes
2answers
63 views

Motivation behind the neighbor-joining distance matrix recomputation

In each iteration of the neighbour-joining method of phylogenetic trees construction, after joining the nearest neighbours the (additive) distance matrix $D_{m \times m}$ is recomputed as $$Q_{ij} = (...
2
votes
1answer
758 views

How can I plot multiple sequence alignment in R as a heatmap

I have many amino acids sequences in a fasta format that I did multiple sequence alignment. I was trying to plot something like binary a code as heatmap. If it had a change in the AA compared to the ...
1
vote
1answer
66 views

How to change sequence format in my alignment file?

I have fasta file with alingned several sequences (from MUSCLE), when I open it (e.g. notepad++) they look like: And I want dot format of identities like and then save it in txt file. I failed ...
1
vote
0answers
33 views

setting BLAT alignment parameters to give long matches

I'm using BLAT to align DNA sequences between similar species, and having trouble setting the parameters to return only significant matches along the 50bp query lengths. Using ...
1
vote
0answers
33 views

Available Protein sequence alignment dataset and HMM model

It may better to move the question here. I am new to biology and I find my algorithm may be used in the Protein sequence alignment, since it is a henced HMM model. I find that people use HMM to ...
0
votes
0answers
23 views

Determining a Gene's Unknown Function

I'm a beginner in this field (so pardon my rudimentary knowledge/explanation) trying to understand ways on how I could potentially identify genes of unknown function. I am trying to get as close as I ...
1
vote
1answer
67 views

How to align Illumina DNA seq reads to CDS?

I have the CDS sequences for my genome. I want to align Illumina DNA seq reads from related fungal strains to these. This is to identify SNPs in just the coding sequences. I am not sure if I should ...
2
votes
2answers
64 views

How to remove sequence reads contains more than 2 X from multifasta file?

I have 5000 protein sequences in one multifasta file. I found more reads have gaps as X in their reads. So, want to eliminate those reads completely (Whole protein seq) from the file. I am keeping ...
3
votes
1answer
22 views

Passing custom distance matrix to T_Coffee

I am trying to pass a custom distance matrix to T_Coffee, as per the docs, but can't seem to get it to work. The documentation says to pass a matrix like this using BLAST format https://tcoffee....
1
vote
2answers
101 views

How to combine two Genome-wide Association Study (GWAS)? [closed]

I did a GWAS analysis in the past for antibiotic resistance of E. Coli and the results were interesting (matching the literature). I did a new GWAS analysis for some new samples, but the results are ...
1
vote
1answer
66 views

merge the matrix from computematrix of deeptools

I have several matrix from computematrix of deeptools. I need to merge two of them using "computeMatrixOperations cbind -m input1.mat.gz input2.mat.gz -o output.mat.gz" but I am running to error "/...
2
votes
1answer
164 views

MSA (protein) with biopython or something else?

I am very new to bioinformatics (and python in general), but I would like to use python to more efficiently analyse enzymes both in terms of structure and functio, using Jupiter notebook. I would like ...
4
votes
0answers
73 views

What does it mean if aligned genomes are not of the same length?

I am aligning 4 genomes of Psuedomonas chlororaphis using progressive mauve software. Command used: ...
0
votes
1answer
180 views

Can I use BioEdit to quantify the sequence similarity?

I am using BioEdit. It can perform an align of multiple sequences. Can this sequence similarity be outputted as a value, e.g. 70%?
0
votes
2answers
106 views

How to make Venn diagram for the Macs peak calling output of two data sets?

I have two outputs of macs2 peak calling for two of my data sets. I wanted to plot the Venn diagram to see how many peaks are shared. I mainly work on Unix/Linux. Do you know any way that I can have ...
2
votes
1answer
117 views

What is the meaning of these misaligned reads in a sequencing run?

I am analyzing some SARS-CoV-2 sequencing runs abd often find read alignments like the one in the image. ...
1
vote
1answer
44 views

Finding discriminating positions for a sequence alignment column

I don't have any theoretical background in biology, so forgive me if my question is a bit.. well..dumb. I'm trying to use a Monte Carlo approach to find the discriminating position of a given sequence ...
1
vote
0answers
37 views

Unmapping Alternative reads in BAM file

I want to do some HLA typing, most of the tools require the bam file is aligned to primary genome without alternative read handling. From the International Genome Sample Resource project, I can get ...
2
votes
0answers
166 views

Platanus-allee phasing fail: Error(13): Error, SolveDBG exception!

I am using Platanus-allee 2.2.2 for heterozygous genome (~500mb) assembly with Illumina short reads and PacBio reads input data. I have the file contigs.fa from short reads but phasing step with ...
1
vote
1answer
116 views

plot correlation between several bam files

I have several mab files from medip-seq. they supposed to be replicates and I have to draw their correlation. First I used multiBamSummary from deeptools to merge all the bam files based on bi/bed. ...
1
vote
2answers
2k views

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 ?
8
votes
2answers
182 views

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 software used for ...
3
votes
1answer
539 views

Are the conclusions in "The proximal origin of SARS-CoV-2" legit?

I don't have any background in genetics and bioinformatics, so I ask you if you think that the arguments provided in the article The proximal origin of SARS-CoV-2 by Andersen et al. are convincing. In ...
3
votes
1answer
66 views

Overlap in Paired-end Reads for Sequencing?

Regarding Sequencing: Do/can the paired-end reads have overlaps?
1
vote
1answer
52 views

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?
1
vote
1answer
198 views

How to do BLASTP for short sequences (<20 aa) effectively?

I am trying to find sequence homology between viral sequences and my protein of interest. I have the sequences of their epitopes which varies from 5 to 500 amino acids long. For shorter sequences, it ...
1
vote
1answer
48 views

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?
-2
votes
1answer
149 views

Algorithmic investigation of viral proteins for vaccine design [closed]

I wish to investigate how a virus could be attenuated through targeted mutagenesis by a priori prediction of attenuating amino acid mutations. In particular, I am seeking bioinformatic solutions where ...