Questions tagged [sequence-alignment]

A computational technique to compare two nucleotide or protein sequences. There are two basic types of sequence alignment i.e. local alignment (local comparison of subsequences) or global alignment (end to end comparison of the entire sequences).

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Aligning two PDB structures with different numbers of atoms

What options do I have to align two PDB-files of ribosomes but with different number of atoms? I need to do the alignment using selection "name CA or name P", because the ribosome has both ...
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Alignment given two sequence

I have two sequences and I need to perform sequence alignment to determine all possible sequence alignments. I have created the matrix and managed to find 16 alignments. I wanted to understand if I ...
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How to align more than 2 sequences with Needleman-Wunsch?

I have a DNA sequence of a protein and around 1200 zinc finger target sequences. These zinc finger target sequences are 9 bp long, resulting in BLASTn not finding them in the sequence. Needleman-...
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Is it OK to use predicted protein sequences from RefSeq for protein sequence alignment?

I'm doing a project, and my goal is to do alignments of a particular gene product to see if there is any conservation of secondary structures across different species. So far, I have found a few from ...
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How to make Needleman-Wunch algorithm work if I restrict the number of gaps?

For example, I have two sequences (one is longer or equal to another) and I want to make a global alignment between them, but I only want to generate gaps in the shorter sequence. I see that the ...
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What is limiting the accuracy of genome sequencing today?

What are the current limiting factors of genome sequencing accuracy? By accuracy I mean a closeness relation between the sequenced genome and the finally assembled (I am not sure whether there is a ...
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What is the relationship between a "main" strain genome and its variant genome in archaea?

I am going to analyze DNA sequencing data in order to try to extrapolate some information about the survival strategy of Pyrococcus Furiosus to gamma irradiation, as maybe you already know from all ...
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What is the typical arrangement of amplified genes in archaea genome?

I have to check if some genes are amplified with bioinformatics tools, but, in order to do it, I need to know what this means from a biological point of view. It seems not so difficult to understand, ...
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Calculating sequence divergence score for a protein from identity or similarity score?

I have % identity and % similarity scores for ~50K protein alignments, that I fetched from Ensembl Compara database. The issue ...
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What does genetically tractable strain mean?

I want to study the properties of Pyrococcus Furiosus in surving to gamma irradiation by exploiting the analysis of DNA sequencing data as a bioinformatics study. Before learning how to analyse this ...
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Using BLAST for molecular replacement in structural biology

This is my first time trying to do molecular replacement to solve a protein structure. I am using the NCBI blastp program to find suitable search models. When choosing a search model, I understand ...
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Expected number of mismatches between two alleles of a gene in a population?

I can't find any article about the expected number of mismatches in alignment of two alleles of an assumed gene. Any reference or information about allele mismatch ratio (in a species or higher taxa) ...
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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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in order to align genome multi-fasta files, do you ignore the chromosome sections?

I want to test my implementation of Needleman-Wunsch on two fasta files downloaded from https://hgdownload.soe.ucsc.edu/. However, fasta files on this site are multi-fasta and therefore are split into ...
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Available Protein sequence alignment dataset and HMM model

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 generate noisy copies of the consensus sequence ...
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Different BLOSUM matrices [duplicate]

What is the difference between different variants of BLOSUM matrices? e.g What is the difference between BLOSUM 30 and BLOSUM 62?
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What tool can I use to align multiple protein sequences to one reference sequence?

I have a protein of interest which is ~300 amino acids in length. I also have around 40 short sequences (all 9 amino acids in length); these are all very different from each other. I would like to ...
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How to reduce the number of sequences in a Multiple Sequence Alignment?

I have a Multiple Sequence Alignment, where there are around 5000 sequences. There also exists many sequences where, there are so much of non-sequenced regions (for instance, AU----CGGGCA--NNNNNNNNNN)....
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How to interpret different results from Clustal Omega and Multalin?

I have been working on aptamers, which are nucleotide sequences. They bind to various targets, in my case a particular cell surface receptor. The people associated with the project performed SELEX and ...
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1 answer
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How evolutionarily conserved are UTRs?

Coding sequences of genes have a certain degree of evolutionary conservation, so that comparisons based on sequences (BLAST, HMMER etc) can be informative. Generally speaking, the more two species are ...
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Which database has the ready made 16S rRNA Multiple Sequence Alignment File that I can download directly from?

In my case, I need the ready made 16S rRNA Multiple Sequence Alignment File for E.coli and use it to generate the phylogenetic tree file in Newick format. I've tried using the one from utexas website, ...
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Sequencing inaccurate at the primer site

The times I have sent a sample to sequence, both the forward and the reverse primer sites, show high inaccuracy while the rest of the gene is correctly sequenced. Because of this, the sequences of my ...
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Consensus symbols in multiple sequence alignment [closed]

I was using multAlin for multiple aligning a set of sequences. The output I and came across included the following documentation (English corrected): Consensus symbols: ! is any of IV $ is any ...
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Confusion about a gene's description

I have a very basic biology question. I am reading the description of gene FAM166A here, and I have no idea what "sequence similarity 166" means. What does 166 stand for, what is this gene's sequence "...
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How to pipe Bwa-mem output without saving SAM file

I'm trying to find circular ARN using the program CIRI2. CIRI2 takes as input SAM file from BWA-mem, but I would like to go straight to CIRI2 output without saving SAM file. Is there a way to achieve ...
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Details of Needleman–Wunsch algorithm

I try to understand details of the Needleman–Wunsch algorithm and use an example from the book [Nello Cristianini, Matthew W. Hahn. Introduction to Computational Genomics. A Case Studies Approach, www....
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What is the difference between contig- and read-based sequence alignment?

I am trying to understand the difference between read based and contig based alignment. Is contig based alignment refer to de novo assembly and then it is align to a reference genome. I am confused ...
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How to convert bwa mem output to BAM format without saving SAM file

I want to go straight from bwa mem alignment to BAM format as I don't need the SAM file and it takes up too much space. How do I achieve this?
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Webtool to design guide RNA (gRNA) for use with CRISPR-AsCpf1?

My goals are to use a free webtool to: Identify guide RNAs (direct-repeat sequence followed by the targeting sequence) appropriate for use with AsCpf1 in order to target a specific segment of genomic ...
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What is the best alignment definition for the Multiple Sequence Alignment (MSA) problem?

For simplicity, suppose that I am penalising mismatches and gaps with -1 and adding a score +100 for each match. Does the optimum alignment of the three DNA sequences ...
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What does chrUn mean in the output from a Bowtie run on human sequences?

After having performed an alignment using bowtie2 and GRCh38 as a reference sequence, I got inusual matches on chrUn. Here a small part of the SAM file: ...
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Is setting high mismatch and gap penalties sufficient to distinguish perfectly mapping reads?

I have a fat pile of 125bp whole genome shotgun reads that have undergone quality control, and I would like to pull out just those reads that do not map perfectly to the genome. When I set extremely ...
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How to detect Single Nucleotide Variants (SNVs)?

This image is obtained from this paper. The description of this image is as follows:- DNA-sequence reads from a tumor sample are aligned to a reference genome (shown in gray). Single-nucleotide ...
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Designing degenerate primers using alignment of protein sequences from other species

I am trying to design a PCR primer for a gene whose sequence is not known. Even the whole transcriptome sequencing done in our lab did not identify that particular gene. Hence, I guess I am left with ...
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Creating BLAST database with nucleotide "place holder"

I have a set of nucleotide sequences that contain some special characters with multiple meanings: H -> C, A or T K -> G or T M -> C or A R -> G or A S -> C or G W -> A or T Y -> c or T I would like ...
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What is the relationship between the e value reported by HMMER and BLAST? (Are they equivalent?)

Both HMMER and BLAST report an e value for alignments. Is it calculated in the same way and - assuming that default settings are used - can they be compared directly (are the equivalent)? If not ...
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Identity and similarity for Multiple Sequence Alignment (MSA) of proteins

I have to do homology modeling for a transmembrane protein (sodium channel) and right now I am in the process of aligning the sequences of the template with the homologous proteins I have found. I am ...
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What is the meaning of "E-value" in the BLAST search?

After reading many pages, I still do not understand the definition. Can someone use simple words to explain me that? https://en.wikipedia.org/wiki/BLAST This expectation or expect value "E" (often ...
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Are there any examples of weighted edit distance genome alignments?

It has been said that weighted edit distance is a preferred way to compare/align genomes in practice, e.g., when identifying genetically similar patients. I wonder if there are some concrete examples ...
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What factors should I consider when selecting a reference genome for mapping?

I am under the impression that the most recent reference genome is typically the best case. What other things should I consider when selecting a reference genome? For example, is there any particular ...
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What is a good multiple alignment of large genome sequences when working with limited hardware?

I need to align bacterial genomes (namely mycobacteria, over 4 Mb in length), and my choice would have been either 'muscle' or 'clustalW'; however these algorithms are too memory demanding for such ...
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Phylogenetic tree with tagging

I'm working for a software company. For one of our projects, we need software to cluster nodes in a phylogenetic tree by a certain kind of similarity and give them a user-defined tag. Preferably, the ...
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Do all multiple sequence alignments employ global alignment algorithms?

Multiple sequence alignments are usually done between sequences of similar length, which resembles best a global alignment. However, I'm not sure at all what the algorithmic background would be in ...
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Finding diploid neanderthal alignment data, looking for ambiguity codes

I'm using Neanderthal alignment data from here: http://www.eva.mpg.de/neandertal/draft-neandertal-genome/data.html Specifically, the .bam files. I would like to find alignments for neanderthal ...
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How does one apply Bayesian inference to quantify a read the deeper you sequence?

For NGS sequencing technology, the "deeper" you sequence given fragments, the more certain you are of what is being sequenced. This sounds like a simple application of Bayes's Rule. What is the ...
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Why does BLAST reduce word size for short proteins?

I'm using BLAST to identify a short protein (BLASTp). If I check the short query then the word size reduces from 3 to 2. However the search will then be less ...
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How to interpret Percent identity matrix created by Clustal Omega?

I did a multiple sequence alignment using Clustal omega. checked similarity for 3 protein sequences : aspartyl aminopeptidase [Homo sapiens], aminopeptidase P (APP) [Plasmodium falciparum 3D7], yeast ...
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why does the score matrix influence the E value (BLAST)

When I align two HBB protein sequences wich have 80% identity, I used two kind of score matrices: Blosum62 and PAM30, to figure out the impact on my results. I noticed that the bit score is higher ...
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How to compare Smith–Waterman algorithm implementations?

Assume that you have two implementations of the Smith–Waterman algorithm (with what ever heuristic they apply to speed up) for local sequence alignment of genomic sequences. I would like to know if ...
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Difference of coverage between amplicons

I have 2 fastq files and I generated BAM file (indexed and sorted) of some reads. I aligned them to a reference genome (hg19). I am working with different primers. ...
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