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.

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BWA-mem and sambamba read group line error

this question has been asked [and answered] on Stack Overflow This is a two-part question: help interpreting an error; help with coding. I'm trying to run bwa-mem ...
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How to remove the unpaired reads in sam/bam files?

I have sam and bam files for the chimeric reads, which come from two different parts of the genome (For example, the first half of the read from part of Chromosome 1 and the second half of the read ...
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How to align integer (non-DNA/protein) sequences?

I am looking for an algorithm to find the "best" alignment between two sequences of integers similar to how one aligns nucleic acids or amino acids for homology comparisons. For example, the ...
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How does split reads look like in sam files?

I used bwa mem to align the DNA with the reference genome. If there are split reads (chimeric reads, come from two different parts of the genome), will it be split into two lines rather than one line?
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How to identify most important Amino Acid residues in a given protein?

Continuing from the title, in my context, important means that changing the set of AAs (either or one more many) changes the domain and/or fold and/or function and/or family etc. I noticed that there ...
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Identification of unique chains in proteins by sequence similarity

I'm trying to find unique chains or proteins within their PDB files. Many proteins have multiple chains, but very often they are identical (say, the PDB file consists of 4 homodimers, for example, so ...
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Multiple sequence alignment with gaps

I'm working on a problem where the elements of multiple arrays need to be aligned with each other. While doing some research on algorithms that could possibly be applicable to this task, I stumbled on ...
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1 answer
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Perform protein structure-based sequence alignment in Python

I am looking for a Python package that performs pairwise structural alignment of protein structures (i.e., PDB files) and returns a sequence alignment. PyMOL is able to do this through the GUI, for ...
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how to create "sample file" for the qAlign() function after trimming the reads in R

I'm an absolute beginner trying to solve this question "Align the trimmed and untrimmed reads using QuasR and plot alignment statistics, did the trimming improve alignments?" I did trim the ...
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Extract SNPs from multiple sequence alignment

I’m wondering if folks have recommendations for tools/scripts to extract SNP sites from a multiple sequence alignment of consensus bacterial genomes? Specifically, I am interested in a multiple ...
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Phylogenetic tree building from proGenomes database for shotgun metagenomics

For some weeks I'm fighting with an issue about phylogenetic tree building to use in a phyloseq object in order to calculate beta-diversity metrics that takes into account phylogenetic distance. I’m ...
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Why must a maximal non-branching path be a contig?

The following is from Bioinformatics Algorithms: Fortunately, we can derive contigs from the de Bruijn graph. A path in a graph is called non-branching if in(v) = out(v) = 1 for each intermediate ...
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What is the different between the I-TASSER, phyre2, SWISS-model in the 3D tertiary structure?

What is the difference between the I-TASSER, phyre2, and SWISS-model in the 3D tertiary structure? How do they get the results? When I did a prediction, I got a similar result for the highest template ...
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How to convert Foldseek .m8 alignment files to FASTA format?

I want to use sequence alignments found by Foldseek in PROSS. I know there are other ways to get alignments (also tried with results of HHPred), but I had in mind that Foldseek may find remote ...
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1 vote
1 answer
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Bowtie2 mapping with multiple indexes

Background: We performed NGS using cells collected from mice in a xenotransplantation study. As such, the FASTQ files contain reads of DNA from both mice and human cells. I expect ~30% of reads are ...
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Where to find asymmetric nucleotide substitution matrix with IUPAC encodings?

I am using the pairwiseAlignment function from the Biostrings package to calculate the distance between a consensus sequence and ...
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1 answer
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Sequence alignment with MUSCLE

For protein multiple sequence alignment (MSA), I am using MUSCLE (v5.1). The default setting without any specifications gives a 'bad' output even though my proteins are very similar (UniProt sequence ...
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Help me to calculate Heaps Alpha value from the roary pangenome pipeline result?

I need to know whether my pan-genome is open or closed. For that, I need to calculate the ...
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BWA mem | samtools view: Intermittent parsing error

Update The issue was that bwa was running out of memory and failing, but that error wasn't floating to the top (see @Steve's answer, below). I was getting an error ...
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Programmatic way of accessing the FASTA sequence similarity tool (or similar) in Python

I am looking for a tool that performs a sequence similarity algorithm for proteins. More specifically, I am looking for something that would be usable in Python (or anything else usable in the command ...
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Samtools sort: most efficient approach to sort a single sample after aligning split .fastq files

Related to my other question (Samtools sort: most efficient memory and thread settings for many samples on a cluster), we need to optimize samtools sort as we ...
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Samtools sort: most efficient memory and thread settings for many samples on a cluster

We're preparing to analyze thousands of .bam files beginning with re-alignment, sorting, etc. Complicated question: Has anyone investigated the optimal thread and ...
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Are there different PAM matrices for different protein families? - How is the inferred common ancestor known to start with?

I am confused about the sequences one starts with to generate the PAM matrices. The sequences to start with are supposed to diverge by no more than 1% (in sequence identity) wrt a common "...
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PSSM Matrix in PSI-BLAST

After running PSI-BLAST one obtains a profile matrix with this header: A R N D C Q E G H I L K M F P S T W Y V How does PSI-...
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ClustalOmega alignment

I am performing multiple sequence alignment using Clustal Omega for 600 RNA covid-sequences, i.e. cDNA on Genbank, with input characters around 30574 characters for each sequence. I am running it on ...
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2 answers
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What is the most appropriate way to find the most recent common ancestor between two distantly related species

I want to specifically find the common ancestor between a lobster and a humans. I suspect it was an aquatic worm of some description. But I want to know about the nervous system of this common ...
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1 vote
2 answers
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Help with MinION sequencing data species identification

Hi I'm new to bioinformatics and have just completed my first run on the MinION (long read sequencing Oxford Nanopore Technologies). I was hoping someone could direct me towards R packages, workflow, ...
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Why does Nucmer Genome alignment produce faulty Dot plot?

I am using Mummer v.3.23 to make a dot plot between two genomes of the same species. One genome was assembled using PacBio and one from Dovetail. None of them is ...
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MarkDuplicatesSpark failing with cryptic error message. MarkDuplicates succeeds

I have been trying to follow the GATK Best Practice Workflow for 'Data pre-processing for variant discovery' (https://gatk.broadinstitute.org/hc/en-us/articles/360035535912). This has all been run on ...
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Extracting Sequence Unique to a Certain Genome

I have two genomes with high similarity. But I found out that one genome has a longer sequence of about 200 kbp. I try to align the sequence with Mauve. How can I extract this unique 200 kbp?
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replacing periods with hyphen

I am a software engineer and not a bioinformatician. I am looking at some code where they are looking at aligned proteins that are in the A2M alignment format (https://compbio.soe.ucsc.edu/a2m-desc....
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4 answers
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Remove gaps from alignment?

I have an MSA (protein sequence) and I have used various programmes (Clustal, Aliview, MEGA11 etc) to align. However, in all programmes I get many gaps which is not ideal as I am trying to construct a ...
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How to compare sequences of genes obtained after whole-genome sequencing to reference genome?

My idea is to align whole-genome sequencing data (as fastq files after, 30× coverage, gDNA) to the reference mouse genome (NCBI), extract the immunoglobulin locus and compare it to the reference. I ...
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Global vs Local alignment scoring matrix

When creating scoring matrices for global and local alignments is there are difference regarding the "highest score of the matrix". For example, for the two matrices below, the correct ...
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pysam "Exec format" error

I am a beginner and trying to read a bam file in Python. The lines below throw the error ...
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2 votes
0 answers
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Bowtie2 gets stuck on alignment

I am aligning a fastq file as follows: ...
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1 vote
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Colouring amino acid substitutions by scoring matrix

I have a list of site-specific amino acid substitutions from a mutagenesis experiment which I am visualising by colouring the structure of the protein in PyMOL. I would like a way to colour the ...
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Type and number of gaps in sequence alignments

I used Kalign and Muscle to align given sequences, the results are presented below. My question is, based on the two alignments which tool seems better? I would personally believe that the Muscle tool ...
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2 votes
1 answer
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blastn returning an inferior alignment

In my work I've found that in circumstances where there is a mismatch near the edges of the query sequence, blastn prefers to return a shorter contiguous alignment, rather than allowing for a mismatch ...
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1 answer
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Given two ADN sequence, can there be multiple optimal alignement? And how to optimally find them?

Given two sequences, I know we can determine optimal alignment of sequence with the Needleman–Wunsch algorithm. But is it possible that two alignments have multiple optimal alignment (I guess it would ...
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2 votes
1 answer
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mpiblast alternatives?

I am looking for a sequence alignment software capable of pairwise alignment of a large number of protein sequences (10^7). I tried to go for mpiblast: https://wiki.canterbury.ac.nz/display/UCHPC/...
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Does the alignment need to be redone when using SAW method to test long branch attraction?

I am looking into different methods to test the long-branch attraction problem. In this chapter they talk about the SAW method - excluding one and the other taxa from the dataset and see if they ...
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4 votes
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How to get phylogenetic tree from multiple genes?

I constructed a phylogenetic tree using a gene (example - secA). I had to gather the same gene sequence for all the required species from public database-NCBI and then constructed the tree after ...
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How likely is it to find primers sequences in already-trimmed reads?

So, I am analysing 18S amplicon data (fastq files) to be able to eventually investigate the taxa composition. After removing primers (using cutadapt) from both R1 ...
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-2 votes
1 answer
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Where to find rat genome for STAR alignment?

I'm trying to find the rat genome to carry out STAR alignment for several FASTQ files. Where would I find these files?
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-1 votes
1 answer
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Alignment statistics

Given a multi-fasta multiple sequence alignment file, is there a quick way/tool to calculate average pairwise sequence identity? Even better, given a whole genome alignment file (...
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1 vote
0 answers
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How to modify dot plot in MUMmer 3 for bacteria comparative genomics?

I was trying to make a dotplot to visualize genome-genome sequence alignment by using the MUMmer 3 software (it is typically used to compare whole genome sequences of bacteria). I runned the same ...
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2 votes
2 answers
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What is the file .mums created by mummer?

I am doing genome sequence alignment using MUMmer, in particular I want to do a dotplot with mummerplot. So the passages that I did are: 1.create a file .mums with the following command line: ...
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4 votes
1 answer
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How do you convert Raw Alignment Score to Bit Score?

I'm coding a pipeline where I make a lot of pairwise alignments, and I end up with raw alignment scores. But, I really need to look at my results in terms of bit scores. I know that the formula is: $𝑆...
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0 votes
1 answer
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Smith-Waterman traceback with large gaps

I am currently trying to understand how the traceback algorithm is supposed to work for the smith-waterman algorithm as my current understanding breaks down in case of a large alignment gap. Assume ...
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