Questions tagged [alignment]

These questions are about sequence alignment.

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20 views

use Kallisto in galaxy

I want to use kalisto for sequence alignment in Galaxy. i found this field empty: there is no option available for the reference transcriptome. how I can get one? Can I let the other configuration by ...
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1answer
17 views

Total pairs of amino acid substitution

I am reading a blog and it says: The numbers for identities and replacements used for calculating the overall alignment score in the expression above are usually presented in the form of a 20 x 20 ...
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1answer
31 views

where to find sample contig data

Where or How can I find contigs? I am trying to learn Bioinformatics and I want to make a reference-based gene search. I also want to align contigs with a given reference sequence. From NCBI other ...
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1answer
39 views

File format of substitution matrix in clustalw

I need to set the substitution matrix used by command line CLUSTALW when comparing DNA sequences to: 0 -1 -1 -1 -1 0 -1 -1 -1 -1 0 -1 -1 -1 -1 0 from my ...
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1answer
19 views

Understanding ViennaRNA RNAdistance scoring table

I'm trying to compare the output of 2 different algorithms of RNA structure prediction (my implementation of Nussinov vs RNA-mfold algorithm) using the RNAdistance algorithm that is part of ViennaRNA ...
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2answers
73 views

Calculate genome coverage and depth from alignment

I have a .bam alignment file and a genome reference .fasta file. I am looking for a easy to use tool (that I can reference in a publication) to calculate the percentage coverage of the reference by ...
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0answers
87 views

STAR aligner multiple fastq files

I’m using STAR to align fastq files from SMART-seq2. I have raw data folder containing sub-folders with samples names the sub-folders each contain fastq file. How can I make a bash command in order ...
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1answer
42 views

Median string problem & multiple sequence alignment

I read about the median string problem as an introduction to the multiple sequence alignment, however none of the MSA algorithms used seems to be using the idea of finding the median string. To my ...
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1answer
52 views

Global alignment between two sequence X and Y with maximum number of identical matches

If 2 protein sequence X of length m and Y of length n and if there are several highest scoring global alignments, then I want to get one alignment that has largest number of columns in which a letter ...
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1answer
65 views

Supplementary aligments in VAF

This question has also been asked on Biostars I have a doubt, are supplementary alignment usually considered when the variant allele frequency is calculated? Thanks a lot. In my case I have some ...
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1answer
65 views

Assessing PyMol sequence alignment object

I use cealign in PyMol for structure alignment. Instead of visualization, I want to return the alignment object to my python script for further analysis. Is there a function to return the object ...
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1answer
27 views

Measure the purifying selection for certain taxa along a phylogeny

I am posting this message because I need clarity about the analysis I want to perform. In my analysis, I have a homologous gene in 13 species, and I would like to evaluate the selection pressure of ...
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6 views

Mutated residue number shown wrong in foldX yasara

I am trying to mutate phenylalanine 274 position in Uracil DNA glycosylase with alanine. The pDB file has the protein starting from 82nd residue. After the repair the console shows FA161A. The residue ...
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28 views

Why do I get cytosine to guanine/adenine transitions in bisulphite treated sequences?

I got my sequencing results (bisulphite treated and non treated sequences of same species Allium cepa) and now I have to do analysis in Cymate online tool. I prepared all sequences as it is written in ...
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2answers
45 views

What programs account for structural alignment of different parts of distant homologs which have significant structural differences?

If there is a need to perform structural alignment of different parts of distant homologs, which program one should use? Since distant homologs often have significant structural changes, meaning the ...
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1answer
99 views

TopHat2 versus HISAT2 inner workings

In my intro to bioinformatics course, we mentioned that TopHat2 and HISAT2 will both try to align as many reads as possible to the reference genome (TopHat2 has been superseded by HISAT2). For the ...
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31 views

BAM file filteing to remain best isoform

I ran HiSat2, MarkDuplicate, removed reads with the lower quality score than 40 and finally only kept properly paired reads. After the BAM filtering steps, I used the Scallop results with TransDecoder....
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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. ...
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1answer
109 views

why in RNA seq don't we only use reference transcriptome?

I would like to ask why in RNA seq analysis (alignment step) we use sometimes reference genome instead of reference transcriptome? thank you!
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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 ...
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1answer
217 views

Difference between genome assembly and genome sequence alignment to a reference to find structural variants

I'm trying to determine what the difference and benefits of genome assembly and genome sequence alignments are when trying to identify structural variants or transposons in populations. I've been ...
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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 ...
2
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1answer
233 views

How to extract unmatched reads using bwa and samtools?

I have a single read (NOT paired) that I need to pass through the workflow described in Beauclair et al. paper (free version here https://rnajournal.cshlp.org/content/24/10/1285.long) for identifying ...
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1answer
205 views

Can't align 2 sequences, (MAFFT killed)

I have 2 .fa sequenes like: ...
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1answer
24 views

which is the right prosite pattern?

I would like to ask if the right Prosite pattern for this multiple alignment: Is it this: A-T-[AT]-G-x-C-[AGC]-C-x(1,4)-A or this: ...
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1answer
113 views

How to calculate mutation rate and mutation sites in a genome using FASTA file?

I have 6 viral genome sequences of the same virus and 1 reference sequence in FASTA format. How I can identify mutations and mutation sites in those genomes using FASTA sequences but how I can do ...
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1answer
65 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 ...
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1answer
78 views

Why use Needleman-Wunsch if there is no way to evaluate the statistical significance

I thought that Needleman-Wunsch is the best approach to align sequences. However, I read that it is impossible to evaluate the statistical significance of the alignment if you do global alignment. So ...
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1answer
63 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 "/...
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0answers
81 views

How can I interpret multiple alignment results?

I would like to ask how I can interpret objectively multiple alignment results. I have used JALVIEW and TCOFFEE. I would like to ask if consistency score plays any role in the interpretation? I ...
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1answer
88 views

What's the meaning of having different alignments with the same qname in a bam with no duplicates?

I have removed duplicates from my bam file (not secondary, nor suplementary alignments), and then I have looked for some repeated qnames (to assess the failure of a ...
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1answer
76 views

Chromosomal order of supplementary alignment in BAM file “SA” tag

I have several long-read sequences, which when aligned to a human reference genome, aligns to multiple chromosomal fragment as a result of chromothripsis shattering the linear DNA and randomly piecing ...
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2answers
117 views

Extract end position from CIGAR

I was wondering how could I obtain the end position of an alignment using its start position and its CIGAR String. If an alignment present some soft clipping, for example: ...
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0answers
36 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
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1answer
63 views

Translating a genome sequence into possible frames

I have a sequence below from MYC gene about which I need to translate the sequence in all possible frames AND identify (for each frame) which codons are actually used in MYC ...
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0answers
34 views

Given a multiple sequence alignment, how do I output all of the non-consensus characters by location?

I have an MSA from MAFFT (as a FASTA file; there are several sequences in the MSA), and I would like to quantify the "variants" between these sequences. What is the standard tool to do ...
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1answer
44 views

choosing a good representative genome subset

I'm trying to build a genomic database for DNA alignments. I started with NCBI accessions, but the data is very multiplicative, so I want to use subset of [max] N different strains for each specie. my ...
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1answer
36 views

Running tophat dockerfile in background

I need to use tophat2 to align some sequences, and I wish to use the docker container. These are large sequences so it will take a long time, plus I'm working on a university server so the chances of ...
2
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3answers
91 views

Make a fasta out of mapped reads without taking into account the reference

I've aligned reads onto an haploid reference genome. I'd like to have a consensus sequence of all my aligned reads that doesn't take into account the reference genome I used (i.e. I just want the ...
2
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1answer
144 views

How can I not show insertions in the Integrative Genome Viewer (IGV)?

I am using IGV 2.5.2 and would not like to see the insertions in my aligned reads. How can I do that? I have managed to remove mismatched bases because there is an option to do so when I right-click ...
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1answer
76 views

Use of Electronic Phenotype in EHR

May I know what's the use of Electronic Phenotyping using EHR data? I did refer this link but have few questions I understand that ...
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1answer
63 views

Is there a modern alignment tool tailored for transmembrane regions?

I am looking for a project or tool that allows programmatic pairwise alignments of proteins but that takes care with transmembrane regions of proteins. TM regions are traditionally too information ...
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3answers
67 views

Is BWT based aligner suitable for any types of alignment task?

Burrows wheeler transformation based aligner like BWA or bowtie seems a standard alignment tool used many area. I was just wondering if there is a kind of alignment task in which BWT algorithm is not ...
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0answers
191 views

bedtools coverage - Report the depth at each position in each A feature

I am using bedtools coverage to compute the sequencing depth at every positions of a chromosome but it didn't work as I expected. Instead it reported 0 coverage at every positions. This is how I did ...
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2answers
647 views

Error with BWA Mem input having multiple fastq files using cat and process substitution

Running BWA Mem on a number of paired end fastq files using process substitution on the inputs results in this error: ...
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1answer
150 views

BED file from .bam alignment structure

I am using a pipeline from nanopore to detect structural variants (SVs) in a human sample with long-reads sequencing. The first steps of the pipeline are: index the reference genome with ...
2
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1answer
175 views

What do the symbols mean in minimap2's gap cost equation?

Heng Li's paper on minimap2 is understandable to me right up until the moment that it gives this definition of gap cost: 2.2.1 Alignment with 2-piece affine gap cost Minimap2 performs DP-based ...
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1answer
164 views

Read alignment using Bowtie2

So this is related to CRISPR-CAS9. I am working with off-target predictions for my thesis and was looking at all scientific papers related to CRISPR. I found one and decided to use their datasets. The ...
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2answers
132 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: ...
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2answers
370 views

How can I find out if my gene of interest is duplicated?

To identify homologous genes, I performed tBLASTn analyses against my genome of interest resulting in sequences of a closely related species. Using this method, I found two (and in some cases up to ...