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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How to add bootstrap values to the phylogenetic tree generated by OrthoFinder?
When we run the OrthoFinder analysis tool on a group of genomes to get the orthologues shared by them one of the output files include a folder named 'Species_Tree' that contains a text file named '...
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Mapping statistics from the bam files
I would like to find the mapping statistics from the sorted bam files.
Samtools flagstat gives the output only for a single file. What is the easiest way to find the mapping statistics for all ...
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Automated method to figure out whether a recognition site is conserved or not using the results of simulated restriction digestion
Restrict from EMBOSS Suit version 6.3.1 with the following
parameters: snucleotide1, sitelen = 4, rformat = table, enzymes =
enzymes.txt.
From the 4379 enzymes present in REBASE, we selected the 650 ...
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Seeking Guidance on Designing DNA Sequences with Specific Criteria
Dear Bioinformatics Community,
I hope you're all doing well. I am currently working on a project that requires designing a DNA strand or more, every 10 nucleotides long (preferably), with specific ...
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RNAseq alignment: best practices for aligning to multiple isoforms?
I have Illumina RNAseq data and would like to maximize my power to find candidate genes that are differentially expressed genes between experimental conditions.
Many of my (de novo assembled and ...
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Is my reference sequence too small?
I'm trying to map ONT long reads to a portion of a gene I'm looking at. The region is about 25bp long. When I search for the region in the document it pulls up the sequence in every read but when I ...
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Add or Simulate Noise in Short-Read Paired End Data
For a project I'm working on, I need to figure out how to model noise that may be happening in real genomes due to alignment errors, contamination, etc. Specifically, short-read paired-end data either ...
Suraj Rajendran
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Sanger Sequencing Knitting Error
I am doing a project where I am reproducing the analysis from the article "sangeranalyseR: Simple and Interactive Processing of Sanger Sequencing Data in R". Below is the example chunk for ...
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Phylogeny building in R from FASTA files:
Im working on building a phylogeny from scratch with downloaded FASTA sequences from GeneBank. I think Im doing alright up until the multi sequence alignment in the ...
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How do I build the MinusB database for Kraken2? (Taxonomy issues)
I am attempting to build my own custom database for Kraken2. I have two questions:
If I have the MCPyV genome in a file called MCPyV.fasta, how do I build a database with just this?
How do I build ...
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How is the "canonical" version (`_entity_poly.pdbx_seq_one_letter_code`) obtained in the PDB?
I encountered the dichotomy in the context of PDBx/mmcif files, say, 6OSQ: each chain has a
_entity_poly.pdbx_seq_one_letter_code...
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Read Clustal file in Python
This question was also asked on StackOverflow
I have a multiple sequence alignment (MSA) file derived from mafft in clustal format which I want to import into Python and save into a PDF file. I need ...
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Maximum likelihood estimation for tree construction
Could someone direct me to a resource (textbook chapter, lecture notes, online video, etc.) that demonstrates, in a mathematically or computationally rigorous way, how to use maximum likelihood ...
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Matches, mismatches and indels
I have a bam-file of reads and reference genome. How can I located matches, mismatches and indels in three different files with Phred score in each data of the files?
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heatmap of specific sequence motifs in aligned fasta files
I have a collection of fasta files, each containing three aligned sequences. I am interested in understanding the distribution of a specific sequence motif PGP, RGP and KGP in all the alignments. I ...
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How can I align two novel sequences to a reference genome and build a phylogenetic tree?
I have two new amino acid gene sequences that I want to align to a reference genome. Is it a good idea to have a combined phylogenetic tree? what will this type phylogenetic analysis called?
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How to identify sequence origin in DNA shuffle reads?
The data
I have a large number of reads from sequences that were generated by randomly shuffling regions of two parent sequences together. See the following image:
The regions that are shuffled are ...
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Why does the Smith-Waterman algorithm have a complexity of $O(m^2 \times n)$?
I recently read that original the Smith-Waterman algorithm to do a local pairwise alignment of sequences has a complexity of $O(m^2 \times n)$, where $m$ and $n$ would be the lengths of the sequences ...
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What can be the bias of aligning paired-reads in a single-end mode?
I don't know if I'm in the right place but I have a technical problem to fix. I would have to align paired-end reads from Illumina sequencing to compare a normal genome with a tumor one.
When I align ...
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Aligning PacBio HiFi reads to reference genome using pbmm2
I am trying to align a yeast strain sequenced by PacBio HiFi reads to the reference genome S288C (https://www.ncbi.nlm.nih.gov/data-hub/genome/GCF_000146045.2/) using pbmm2 but for some reason I am ...
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How to calculate average BLOSUM62 scores?
I can understand the motive behind the BLOSUM62 matrix, this being a pairwise mutation matrix describing aggregate mutations between the 20 amino acids.
However how would you calculate the average ...
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Relationship between molecular weight and linear peptide
Sorry for this very beginner homework question:
Which of the following linear peptides is consistent with Spectrum = {0 71 99 101 103 128 129 199 200 204 227 230 231 298 303 328 330 332 333}? (Select ...
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How to chop fasta / bed /peak file genomic segments into smaller fixed or custom genomic intervals
I am trying to split my .bed/.fa file genomic segments into arbitrary smaller overlapping intervals:
Consider a typical line/row in my *.bed file as follows:
chrom. $\ \ \ \ \ $ start $\ \ \ \ \ \ \ \...
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What is the best way to process yeast genomes?
I have obtained several hundred raw, unassembled yeast genomes from NCBI and I am looking for advice on how to process the genomes for downstream analysis.
I have a reference genome (S288C) to use for ...
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The difference between sequence-independent and sequence-order independent structural alignment?
I am confused about the difference between sequence-independent and sequence-order independent structural alignment. TM-align for example claims to be sequence-independent; however, I've seen it is ...
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How to convert fasta alignment to nexus or phylip format?
I generated a multiple sequence alignment using mafft, but I would like to convert it to nexus or phylip format (required by a downstream software). What's the easiest way to do the conversion?
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PyMol alignment script
Is there a way write a script in python to use "super" to align proteins from a 2D array? Each row of the array has 2 columns, and for each row, I want to "super" the two proteins (...
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Lower case vs. upper case nucleotids in sequence vs. dots at the end
What is the difference between lower case and upper case nucleotides in a sequence? My other question is what are the dots at the end of the sequence? Some examples are shown below:
GGgG,GGgG,GGgG,...
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How are BLAST record scores calculated in biopython
Can someone explain how the score is calculated for Bio.Blast.Record.Description? For example, if Record.Description.num_alignments is >1, is ...
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How can I find the maximum percent identity between two sets of (unaligned) sequences?
As the title states, I've got two sets of unaligned amino acid sequences (~25k sequences in one, ~3k in the other). I want to find the minimum distance between a sequence in the first set and a ...
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STAR vs Bowtie2
What is the fundamental difference between STAR and Bowtie(2). Specifically, what is the difference in their final output (regardless of run-time differences, speed, memory usage etc.). Both seem to ...
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Most reads no_feature with htseq-count
I have mapped reads to the yeast (R64-1-1) genome with STAR like this:
...
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Multifasta protein alignment
I have around 4000 orthologous proteins for each of 5 species, I'd like to align them and to concatenate alignments. Which tools can I use? And how?
Marco
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Statistical significance of pairwise protein sequence alignment
I have identified a conserved region in a protein I'm studying, by doing multiple sequence alignments against a dozen of its orthologs. I've then found that this region also aligns relatively well ...
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Aligning scRNA-seq fastq to .bam without cell barcodes
I would like to convert the fastq files from this dataset: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE98679 to .bam files. The group did not provide the scripts they used to to their ...
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Problem with sequence alignment
I'm trying to find if the peptides in column A are present within the longer peptides of column B.
Pairwise alignment tools take the data from both columns as one string (i.e., TIIDYTNNHYTNNHLEII... ...
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multi-sequence alignment of samples with multiple contigs each
I want to perform a multi-sequence alignment on 12 samples that clustered based on cgMLST. Ultimate goal is to find out whether they differ by the presence of a few genes.
I have performed multi-...
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What tool I can use to map short-reads sequences to reference genome and get specific mapped size
I have about 300 90-bp sequences which I would like to map to a reference genome to make it longer to a 300bp sequence, wherein the 90bp is at the middle.
Anyone knows what bioinformatics tool I can ...
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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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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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Select synonymous sites from a multiple sequence alignment
Could someone kindly recommend a tool or R package that can identify synonymous sites in a multiple sequence alignment?
I wish to select those taxa for tree reconstruction and other downstream ...
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